The deep pits on the vertical surface here are concerning.. Red flag Number one. You don't normally see such pits on vertical surface. This is where I would have broken out the ice pick and find out exactly how solid things are.
Red flag number two is holes appearing when media blasting, especially that far up on a panel. Again, this is a case where I break out the ice pick and see how solid things are.. Your post is a good case in point that seldom are pits an isolated occurrence.. This also suggests you need to check out everything inside the cab for other rust areas.. It came from somewhere.. The rust inside on the lapped panels is likely from condensation drainage. The seam sealer you saw is likely similar to that I have seen, installed hap hazardly where water intrusion or entrapment is entirely possible. But it doesn't explain the pits on the outside surface of the door jamb.
Red flag number 2A... If you weld up a pit there are likely others in the general vicinity. The electrical current that the panel sees from welding will activate those hidden pits where they will come through more quickly than had they not been exposed to the current. The ones you didn't find will come through your fresh paint job within about two years.. Not that it shouldn't be repaired, but it may need more extensive work than you had planned. In my shop that lapped area would be opened up to see exactly what is there..
Metal repairs are cheaper before your final paint finish goes on. Find out how extensive the damage is now..