Should be fine. The only problems you'd run into (off the top of my head) is 1, In SP skirmish the standard starting ship won't be there. You'll always have to select a ship for the added races. 2, Either the added races will have ability to double engines, or if you disable engine doubling in the game then the Orions won't have it like they should. 3, You'll have ship schematic/ui inconsistencies. The Lyran ship displays won't work in the pirate slots, for instance. 4, You'll have to redo the campaign .mct files if you don't want the added races to do the pirate campaigns. 5, The added races won't be able to flip hexes on the empire's map. I've tried everything that I could to change that, but nothing I've done has worked.
That's all I can think of right at the moment. Nothing too major, IMO, except for the engine doubling thing.