[leegreen]

I'd assuming popeye has clean metal either side of a new seam with pinholes in the new weld, not rust pinholes
If you rely on the filler in a spot where your seam is flush or proud, once you sand that filler all you will have left is a tiny plug of filler in the pinhole. Will it stay put and stay sealed? I'd get after the pinholes you can. But inevitably there are going to be some you miss or can't see. Unless you do wray schellin quality work.
The important thing is to seal well with primer and paint including sealing the backside and keeping it sealed. And for hard to get to areas do some rust preventative like a grease with oxygen inhibitors, or a waxy non drying rust preventer. or a toilet ring melted into some oil.....anything except one of the 'rubberized rust encouragers' that are so popular with people reselling cars