have you considered using Por15 first before the filler.
It's used widely in classic car restoration.
For surface rust areas...that you are not cutting out..
Grind down well, use the marine cleaner to clean the metal, use the metal prep spray as directed, then put Por-15 over it.
before it dries (2-3 hours), put on a coat of regular primer..... then you can start bodywork again as normal....
It's used on frame rails, suspension pieces etc that are naturally rusty...
dries rock hard, and air tight... thus stopping the rust.