Is it possible to use different source engines and mods on the Steam versions of Quake, Quake 2, and Quake 3 Arena? Are they any more difficult to implement than on the retail, boxed version of the game?
No they are not, you just need to copy the complete game directory to someplace else and do whatever you want to do with it.
I modded Q2 to R1 Q2 and Q3 into CPMA in this way.
i only remember there was a discrepancy of the Steam version of Q3 on where the key file was located, but I do not remember the details at the moment.