MechAssault divided all the 'Mechs into two variants of the same model with different weapons; Clan/IS name for the Clan 'Mechs, and IIRC, also a few IS Mechs(they called the alternate version of the Catapult, the
Bowman, which is...kind of similar).
The Unseen are really only a problem if you're either selling or otherwise 'official', to my knowledge.
MekTek had their mod to add the unseen Marauder, Marauder II, Archer, Warhammer, Shadow Hawk, and Wasp(possibly more, but don't spring to mind) in MW4: Mercs, many of them for years, until they were tapped to distribute MW4: Mercs for free, which forced them to become legally 'official' entities, rather than just an independent modding group.
Also, it's worth noting that only the
Macross-derived 'Mechs are now considered Unseen.