OK, so you have DC/DC power of about 2W. For that power level, a 7x7x3mm inductor is a bit big. Try to work on that, although, I think you can save this as the last step since you have easier optimizations first:
DPAK power transistors are definitely much bigger than necessary - power MOSFET cases have been shrinking a lot lately. I'm switching hundreds of watts of power with transistors half of that surface area! So I think this is #1 where you can miniaturize, since this is not even much power at all.
DPAK regulator - I guess this is for some logic and/or transistor drive. Probably not much more than a few mA? Definitely use a smaller part.
Handsoldering is not a problem whatsoever in these things. You can even solder BGAs, QFNs etc. with a $50 hot air station quite well.
0805 are HUGE. I'm handsoldering 0402 passives all the time. Even though a little bit more tedious to handle than 0603, 0402 is a good sweet spot for easy enough prototyping and good manufacturing yield even in lowest cost assembly houses - and good integration. 0402 tends to easily fit to bypass 0.5mm pitch IC power pins without requiring huge fan out area that gets in the way of everything else, like a 0603 let alone 0805 does.
Are the 2220 capacitors ceramic? If yes, they are super expensive and crack easily, destroying the device. Replace them with some 1210 or smaller. Use several in parallel.
Stacking multiple PCBs might be an answer, but you have a lot of room for improvement before that.
Just take the bullet of handsoldering these things. You'll learn while doing, and it's not going to take long. Expect some unreliable prototypes you need to rework a bit. But aim for commercial manufacturing as soon as possible so that you don't need to do massive number of prototypes.
Basically, do the parametric search on Digikey / whatever you use, and choose the smallest size you can find, for each component. Try to avoid cases where the pins are "under the device" if you are unsure about hand prototyping. OTOH, those are often the smallest, so you may need them.
Do you really need a crystal? Is timing so critical?