Which is how I do it. Only the Quake data files, none of the program files or libraries as the source port has its own.
Create a folder "QuakeSpasm"
Copy folder "ID1", "Rogue" and "Hipnotic" into the Quakespasm folder. You can find these folders in the Quake installation folder.
Delete all files in those folders, excapt the .pak files. Those are the game data files. You need those.
Create 2 shortcuts, quakespasm.exe -game rogue
and quakespasm.exe - game hipnotic
These are to start the mission packs.
Yep, that's just how I have it set up (been doing it that way for many years, though with DarkPlaces myself), works great.
EDIT: Oh, I read you should use -hipnotic and -rogue, as using -game with these two expansions causes the base game's HUD to be used instead of the altered HUD for the expansions (for the new weapons).