Would think overcoat rather than trying to blend the new and the old. The finish will be more consistent but you will retain the factory drips and runs where they were after addressing the surface rust issue, smoothing the transitions from the fixes and the nice original, remove (after documenting) the seam sealers and make sue you have any old oil or grime removed that would react to the new top coatings
Done it a number of times on nice rust free cars undercarriages and trunks
Looks like your off to a great start