Seems like anyone relying on a few critical special parts should just leave some space on the PCB around the part so that you can just replace the pads for one

Seems like anyone relying on a few critical special parts should just leave some space on the PCB around the part so that you can just replace the pads for one part with those for another and then route and jumper the pins to match the functionality of the old layout. It would make the boards a little bigger, but it would make it much easier to replace an MCU with another part. Zero ohm jumper resistors make adding jumpers for routing easy for pick-and-place machines. For small scape manufacturing the added costs would probably be minimal. If you're going to have to redesign the product anyway, might as well make it more survivable while you're at it.