IME with enamel coated wire, stripping goes much better in a solder pot. You dip the end in, then you "swish it around" a bit, and the result is very clean and easy. This movement lets the enamel get stripped away, rather than melting in place and staying on the wire after you remove the heat source. The insulation turns into a little bit of scuz that forms on the top of the pot.
Of course, this isn't gonna help for the second end of the connection when stringing it along with a pen.
This is why I use kynar wire for prototyping where possible. The insulation is much bulkier, of course, but it strips really easily and leaves a perfectly clean, tinned/silvered wire end for easy wetting. And being able to break the insulation cleanly in the middle is a huge advantage. I almost always solder the second end of a connection like a "middle." I break the insulation, solder that second connection, then cut off the excess wire. By doing it like this, you don't have to turn the entire pcb around 180 degrees to get the second connection to take. I do not even use tweezers while using kynar wire, my left hand just holds the wire, sometimes wrapped around my fingertip. My right hand does the stripping and the wire bending/forming, using a combo chisel/stripper. So while I have to change between iron and strip/bend/cut tool, the ability to strip in the middle more than makes up for it, IMO. If doing a lot of wiring, I sometimes put the spool on a reel, near the project, and just keep it going in one long string. But it's normally easier to just pull off a long piece and keep going until it runs out. So when I'm wiring up a project with the 30AWG kynar, my trashbin receives a lot of leftover ends. I have a 1000 foot reel of kynar at my bench, on a dispenser/cutter. I use this stuff quite a lot, both soldering and with wire wrap.
If doing tight connections to IC pins in close proximity, it is often just as well to use bare wire and to keep the wires short. IME, shorts are a much easier problem to see/avoid/diagnose/fix than bad solder connections due to dirty wires. Basically, the possibility of creating a short between wires (and not realizing it) does not really worry me. Airgaps are fine. Conformal coat or box it up when it's done. But I'm not hand-wiring multiple SMD IC's with no protoboard or PCB... that's just not important for me. Anything that involved is easier to do in CAD, making an actual PCB, IMO.
I can relate to all of your points, you have obviously a lot of experience in this area

I'll be trying to deadbug some pins on a WLCSP64 BGA soon as I don't have the facilities to pcb or reflow one for a prototype, and at $0.90 for the mcu if I screw it up, well ... who cares ?
The picture is a 32 QFN STM32F051 using 0.5mm dia bare silvered wire and a soldering iron tip of about 5mm as my fine tip was worn out at the time. It worked fine with no shorts, first time.