Quote Originally Posted by BenAkenobi View Post
That was part of the agreement between ID and modding community, that the various mods all required full version of game to play, hence this "incompatibility".
Mods shouldn't work with the SW version of quake (just pak0.pak), yes, I remember that agreement at the time. But pak tools could open pak0.pak just fine. I've just fired up a windows vm again and pakexplr managed them both and id1.pak too. So the issue seems to be with the from-source builds of the amateur tools on a modern machine.

I think the most likely explanation for why the tools I tried failed is that they make implicit assumptions that don't hold true in my OS X environment and basically throw a wobbly, probably sizeof(int) etc. being larger than expected (not being a 32 bit system)