bad question with some trick answers... Pits as you show can be perforation,(rusted all the way thru) and you just dont realize it. If they are that deep, you have to remember that there cannot be that much metal left.
With that said, lets move on.
Any place on your car that is a lower area such as bottom of a door , quarter, lower fender, rocker... AND if it has pits like this,,,you need to replace the metal. PERIOD.
Roof, and upper flat areas can withstand more 'cheating'. BUT it IS necessary to be certain the metal is clean all the way down into the pit. If it is not , your time has been wasted.
Once clean, use your choice of body filler. (I will remind you, ONLY if it is NOT perforated) Smoothe and prime as needed. I Highly recommend an Epoxy primer as the first coating technique after mudwork of this kind, then follow up with a high build 2k primer.