the only 16bit code in quake is dos dpmi stuff, and the startup code. windows builds contain no 16bit code (except for the 16bit legacy dos exe stub that all 64bit progs still have)
if the i686 version of gcc has the same problem, then its hardly a 64-bit issue.
there are 64bit portability bugs, yes. I remember one in the sprite code somewhere. the qcvm usually works, but if you're unlucky it can blow up quite nicely.
disable the demos, and it'll get into the console/menus without any fixes for the 64bit bugs, but yeah, that's not actually doing anything.