Rust between panels

[Jakes-66-K10]

I'm in the process of converting to a big back window, and wondering if it's worth doing anything to treat the rust that's between the panels. Had I not removed the small window panel, I wouldn't even know the slight surface rust that was there (ignorance is bliss) so wondering if I should even do anything. Since the build I am working on is going for longevity I'd like to take care of anything that may rear its ugly head many years down the road.

How important is this, it's such a thin layer that you can nearly rub it off with your finger... I know that while I have access to this now (here's my chance to fix it) I also realize that every other panel is likely to have this same light rust behind them, but I just don't know about it nor can get to it.

Is it worth fixing before I put the new panel in place? Is it worth dipping the cap to take care of everything between panels that I cannot see?