It's not that they bottom out, the HEAD of the bolt can hit the inspection cover. If you haven't checked it, I would do so before making any phone calls.
Its both. Flex plates aren't all the same thickness. Nut blocks aren't all the same thickness either. Bolts that are too long can dimple the converter shell beneath the block and cause internal damage. There isn't a lot of clearance in there.
There were threads in forums about PTC convertors ballooning too but that was several years ago, about the same time the aftermarket fan shrouds were melting.
