Also, the software is directly compiled to a specific memory size

Uhm, if the software is compiled for a specific memory size, then we have a problem.. (At least, as far as I can tell.)
Any MK2 software revision works with the Mk2 and the Mk2a, yes?
But the Mk2 had 12Mb, the Mk2a had 16Mb.
So, that means than all Mk2a owners aren't using 4Mb of ram.

(I actually know a way around this, but I was curious if anyone else has an answer..)

Me. The devil's advocate.