When you paint before welding, surely the paint gets burnt away once welded ? leaving bare metal.
I try to spot weld as much as possible and this method is far less destructive than mig plug welding.
Where I do need to mig, I apply the paint and then do everything I can to coat any areas where the paint will have burnt off afterwards.
There is only so much you can reasonably do and it would be wrong to assume the car will never rust again. It's all about keeping it away for as long as possible.
I said elsewhere about the blaze 1275GT that I restored several years ago using this method and it has been back recently for other work which gave me the opportunity to check my previous work to see how it was holding up.
there was no evidence of rust anywhere and everything was as clean as the day it was done.
bare in mind this car lives out doors and had done more than 30,000 miles since the first lot of work so it is used.
Hope that answers your question