I think you are correct.
Our 05 corrolla looked like that in spots on the roof (same color paint) and I masked it off as small as possible, sanded, primed, painted, and cleared that little section. been good for 3 years since and because it's smaller than a dime in size it's real hard to tell unless you're really inspecting the paint up close.
Or you can skip that whole process and look on the bright side... gives you another reason to break out the plastidip!
my last two 4runners had issues with rust on the tail gate. Mine all started rusting by the rear window. My last one I did have a body shop repair it but 2 years later it started rusting again.