which mod you use is determined by a write protected variable /fs_game
When mapping, I use a batch file to compile the map and run Trem with the map afterwards. The line which starts Trem includes the parameter fs_game. So, maybe you can just give the mod directory name to that parameter instead of the current value "base". This is the (definitely working) command of my compile batch:
"C:\Program Files\Tremulous\tremulous.exe" +set fs_basepath "C:\Program Files\Tremulous" +set sv_pure 0 +set fs_basegame base +set fs_game base +devmap "somenewmap"
This is a modification of the command that you could try to launch Trem with the mod of your choice:
"C:\Program Files\Tremulous\tremulous.exe" +set fs_basepath "C:\Program Files\Tremulous" +set fs_game nameofmoddirectory
I can't try it right now, so it's just a guess.