The car was probably repainted...
God knows what happened to this car in all this time. It could be rust pits from a distant past that were painted over...however you don't know what has been done to them to neutralize the rust...
If there ar'nt too many of them, a spot blaster does a good job of going to the bottom of cracks and pits without sending blasting sand all over the garage. Len sells a nice one in the store...
I would get to the bottom of those pits before priming...
My 2 cents worth...
Serge