A buble in the filler won't work its way to the surface, and the reason filler should be lesss than a quarter inch is that greater thicknesses tend to fall out; also, the thicker filler doesn't loose its voc's quickly, causing shrinking/mapping as mentioned.
As Jim said, a bubble usually means rutsted trough. That's why I hacked out the back part of my quarter panel in my post "Touch up." The holes hacked in the car were merely bubbles in the paint, and you can see the end result.
To add some hope to the matter, I just went down and shot a picture:
This was also a bubbled area. Even though I have probed the area to check its integrity--it's sound--it's going to take extensive grinding, and the metal will be fairly thin when I'm done.
It will be 19 years this July when mine was painted, so I really cannot complain about the quality of the surface prep. The problem with surface prep is finding a professional who will spend the time it takes to prep the surface. Surface rust is vary labor intensive. Calculate that quality bodymen run 3 to 5 labor hours for each working hour, and it's clear that rust removal is expensive. That is if you can buy real rust removal.
If there is even the tiniest speck of black in the metal, the rust is still there, and it will come back in a short time. The hood and the roof were a layer of surface rust when I got the car. I know that I spent at least 200 to 300 working hours grinding it out--what it took to really get the rust out.
The pictured area wasn't in the batch of rust I grinded out. Except for 3 small spots on the hood, and 3 or 4 on the roof, those areas are still free of rust, even after almost 19 years.
Bottom line: Unless some of the newer weasel pi$$ on the market actually "cures" rust, you're going to find it next to impossible to find a professional who who will actually remove the rust, rather than making it so that it takes a few years to reappear.