What do you mean by this? That you're treating them as just the Pokemon they are without the variation in their name? That's a bit silly, in my opinion, seeing as there are entire groups of trainers and Pokemon that are worthless in a cube if they aren't allowed their special name variation, as some of the best trainers affect only Pokemon with a certain name variation, and some of the best PokePowers/PokeBodies do the same.
Sorry about it, my statement was a bit vague. The Pokemon currently in the Cube that this effects:
Team Magma's Houndour
All benefits and other effects still matter for these Pokemon, except for evolution restrictions. This is mainly what I meant. Normally, Misty's Horsea can only evolve into a Misty's Seadra or Dark Gengar can only evolve from a Dark Haunter. As far as the Cube is concerned, these Pokemon are treated as 'normal', meaning there is no evolution restriction. For example, Dark Gengar can evolve from any Haunter in the Cube and Misty's Horsea can evolve into any Seadra.