yes, but only with some negativ sideeffects.
One is that you can't have multiple vehicles as starting units in multiplayer. Because you have to force the game to give only one MCV for each side.
The AI.ini probably needs new triggers/teams.
All disadvantages i don't know. I've never made a third side. But there are already Mods with more than 2 sides.
More info here ->
Correctly adding the third side to Tiberian Sun