I have poked screwdrivers through little inocent dime sized surface rust spots before… 99% of the time it is not what it looks like on the surface. I will put money on that if you see a dime sized bubble of surface rust, once your remove the paint you will have about a 2 inch + dia circle of effected metal under the paint you cant see from the surface.
Honestly take an awl or a screwdriver and go poke the spots gently. That will tell you if its rusted through or not in 1 second. just dont hit it so hard that if it isnt rusted through that you dimple/dent or distort the panel!