In that case, I can see why you are working hard while starving. The thing that a startup would answer that I still haven't figured out is why would a company that has been in business for over a decade not have experience in making boards, a key component. I can come up with two guesses outside of a startup. One is a switch from through hole to surface mount. The other is a new set of products that use electronics to the extent of requiring PCBs where the old products did not.
For very low volume, it is often better to do it by hand. Like you mentioned, the setup time both initial to teach the machine how to operate, and to switch to that job in the future are quite time consuming. Add in the stencil cost, the time it takes to setup the reflow oven and stencils, and the fact that the machine will make most of it's mistakes on the first few boards/panels made results in additional cost in labor, parts, and expense. In this case, focus on getting good equipment for hand soldering SMD. This equipment will be good for low volumes stuff and also the inevitable rework for higher volume stuff. The keys to good hand soldering is very good lighting. Good magnification for fine pitch stuff. Good soldering equipment. High quality component handling equipment such as tweezers, vacuum pick up tools. Foot pedal operated paste dispenser. In many cases, I can place just as fast as a low end machine with the right setup. I just don't like to do this for extended periods of time which is why I use a PnP machine. When you are done, stick it in the reflow oven and let it work it's magic. You can get away with a less than good setup for a few boards, but when it comes to working a full shift soldering, you really need a good setup. Especially very bright lighting and good optics to relieve eye strain.
If a low volume product picks up in sales, upgrade it to PnP status. Just make sure that all of the designs are PnP friendly for best results. Some PnP machines have the ability to attach a syringe with attached pneumatic solenoid to apply it to the board. You can put paste or glue down where you want it. For the low volume example, you can get away with not getting a stencil for a given board by having the PnP machine paste the pads before placing the parts albeit, you are taking away machine time so a stencil is often a good investment. Better use is for the ability to paste is a new revision with the addition of an extra cap or two or something else simple where other parts aren't moved. The stencil doesn't place paste where is doesn't belong, so fill in the new parts and save the cost for a new stencil. Alternatively, you can use glue to hold parts down. This is the secret for making 2 side component boards where you place parts on one side and run it through the oven. The second run through, the upside down components will be firmly attached except during the reflow portion. This also plays a roll in the choice of reflow oven. If you have a type of oven that will touch the bottom of the board, you will need to make a frame block for the boards/panels to lift them up. Small parts such as ICs and resistors, small caps, will be held in place by the solder's surface tension. The large components will fall off so glue them in place. If a part falls off, use your rework station to fix it and add glue next time. It will take some effort to get 2 side component boards to run well, but it is well worth the effort.
When it comes to pick and place, feeders are very important. Both in how many you get and how many places the machine can hold. You can have 10 different products or more that can run with 1 setup because they use a large number of the same components. Simply formulate a setup plan with all of the products and feeder locations. Simply load the the feeder plan, load product A's PnP file, put the stencil in and set the paster up, and set the reflow oven up. Then run the product A board through. When done, change the paster for product B, Change the PnP program, Change the reflow oven if needed, and run product B. Then C. And so on. If you have boards with similar reflow oven profiles, same it's setup time by running them back to back. This is the kind of thing you can do if you have enough feeders and enough feeder slots. If you run out of feeder slots but have enough feeders, set the later feeders up and simply swap a few feeders out when you need to.
If machine time is a limiting factor you can optimize the placement rate by selecting prime feeder locations for the most popular components such as 0.1uF capacitors and certain resistor values. Usually the closes feeder slots to the actual board are prime feeder slots. The time it takes to move to a feeder location, pick the part up, move to the board, and place can be very different for each feeder slot. Far away feeders take much longer than feeders right next to the board. For long runs especially, it can save a lot of time to move popular parts to prime locations. Notice in the uCurrent video that the locations selected are very close to the board allowing placement rates of roughly 6 parts per second. The optimization is also important for where to place the feeders relative to each other. Notice that the simultaneous pickup picks from specific reels. If not optimized, the head will have to move between picking up the parts slowing down the action. Low end machine often will not have simultaneous pickups but there is still gains to be made from relative feeder locations. There are also machine specific optimizations to be made.
For larger components that need to use the bottom vision as opposed to on the fly vision, remember that the next place after going to the feeder is to the bottom vision camera. This means that the prime location for bottom vision components is different than vision on the fly components. Also notice that the uCurrent video, the machine only uses 2 heads and the placement rate is very slow compared to on the fly vision placements. A tiny fraction in fact.
As for hookups, you need the right hookups. If you have single phase service only, try your best to get single phase machines. It is expensive to get a single to 3 phase converter or have 3 phase service put in. You may need to have dedicated circuits and special high current outlets installed depending on the reflow oven in particular. Nothing will ruin your day more than having the circuit breakers pop.
If your machine needs air, either tap into shop air or you will need a good heavy duty oil filled compressor sized for your needs. If you have shop air service, you need to make sure that there is enough excess capacity to handle your machine. Venturi effect created vacuum uses a large volume of air. Keep that in mind. I prefer to use a good quality vacuum pump as it is more efficient than using shop air. Even if the machine doesn't use it, shop air is still very useful. Also, once shop air is available, others will probably want to put there stuff on it. Make sure that you have some capacity for them if this will happen and also make sure that they don't cause problems by using too much air. This is especially a problem with some blower attachments that use a ton of air. If you do install some shop air, make sure to control condensed water. Usually the level plumbing will be at a slight slope to allow the water to flow. The best options is to have it flow back towards the compressor to a drop down line with the incoming air in a T. This is where the excess water is allowed to drain down to a stub pipe that collects water. Put a valve there to drain the water out of the line. For drop downs to machines and other workstations, the best practice is to use and upside down U pipe going up then back down. This will prevent the T from dumping water into the machine. It is good practice to also have a drain at the bottom of the drop down as well to collect and release any water that does condense there. With shop air, I'm considering adding a refrigeration unit to the shop air outlet. This is called a drier and it will eliminate all water from condensing in the system beyond the drier. The drier will need to be drained of condensed water.
Machine placement is also important. You don't necessarily need to have an assembly line setup. With low end machines, it is a good idea to inspect the boards after placement to fix the mistakes before putting the board through the oven. This can save time over reworking a board later. As for ideas for setting up a line, there are many good youtube videos that show some interesting setups. You can pick up some very useful hints and techniques from many unlikely sources. My favorite on there that I have seen is the Apple Macintosh Fremont California factory. I know a couple people that worked on the original Macintosh. It's funny to see Macintosh computers make more Macintosh computers.