To answer your questions: indeed welding after painting will burn of the paint and leave a bare open spot, with flaky remnents of charred paint. Weldspots are even the first rusting point, as heated metal (when it turns blue on solidification) is a steel type that rusts faster vs the virgin steel around it. So yes, a valid question.
I opted, and bought, a spotwelder exactly for that reason. spotwelds can be made through weldprimer and the weldprimer seals the weld as a small circle around it, having a high zinc conctent. Some spotweld primers even carry bitumen (EuroPAX - I love that stuff.) that doesn't burn off.
You'll be happy to learn that you can reach the entire sill from the inside passenger compartment. Look at the inner sill, and you'll find a 5 or 6 (i think) 20 mm round openings that will allow you to inject the sills with your favorite paint or wax after you weld everything up.
One route would be to paint everything that you intend to sandwich. Then clean comfortably around weld locations to have clean, fresh steel. Then weld away. Next tape up the drain holes of the sill. Pour in 3 gallons of paint, let it sit for 10 minutes, possibly holding something that vibrates to it to shake the bubbles out (belt sander?). Then remove the tape and catch 2,5 of the 3 gallons that you poured into the sills.
Mind you, the sills have a funny construction with the middle sill not reaching down into the bottom: the leading bottom edge is just the inner and outer sill. The intermediate sill is (originally) spotwelded to the outer sill ; but that seam is about an inch higher up vs the leading bottom edge. It's a rust strap as water from the rear glass will follow the inside of the outerskin, and firstly encouter that seam. That is why i choose to pour in a lot of paint, to also rise above, and fully flood (capilliary) that seam. Let me dig up some pics. Also
@nosmonkey has some pics up in his resto thread, though Ahmet (like me) also replaced full sill panels.
second question about the flange hghlighted in red. I'll have to look at my pics. I was quite anal to get those details right, an in my car not a lot was recognisable.