The code has to support it.
WFA uses indexes on entities that other mods have no clue about. Like for instance a big trigger hurt in cancer3 that kills blue, using a trigger_hurt with a "key" wf_team "1" at the red's spawn room (1 being red, 2 being blue).
Other mods don't use that, they don't have the code for the wf_team check, so every player who hits that dies immediately.
Or each team can use the other team's teleporters. Or doors. etc.
some maps are cross-mod compatable, I tried to add stuff in for some maps to work with team arena as well, but i forget which ones work like that. maybe cancer3/halfes/welt but i forget.
Now WFA will use just about any other ctf map, but WFA uses packs and has a different speed of things so it becomes aesthetic.
You can fire up a TC/cpma/osp map in wfa by using fs_game wfa fs_basegame (name of mod directory). you can do the same by switching stuff around (fs_game defrag fs_basegame wfa) but it's gonna be painful.
Now wf fusion uses the q2wf/tf .ent system where all entities in the map are "dumped" into a folder. (example) That .ent file can be edited in radiant to add, change, or delete ents. add triggers even (but not doors/statics/sold bmodels). If the server sees the .ent file in the directory, it loads that entity lump and disregards whatever is in the actual compiled bsp.
I think there's a team arena mod that duplicated how wf/tf did things also, and has some pretty decent documentation on it.
It's a snap to add external entity support for any mod, it's up to the coder to add it. there's a hack tho, which is very fucked up to use, and i always see messages in irc from people who have problems associated with them. I don't even bother answering them, whoever puts up the maps should deal with them, but if you can extract that entity lump, edit it, then run the compiler with -onlyents it will attempt to update the entity lump in the actual bsp.
But i get an average of 1 query a week on irc from people who can't figure out why they are getting strange errors on different maps. (one miscompiled bsp can throw the whole mod off, hiccup the game engine on the server then messing up clients even if the map isn't currently loaded, and no it's not always gensurf to blame).
ask exactly what you want to do tho.