(If it's the Autobot Bros from RID you're refering to, the super modes were through being charged up by the Matrix, via Ultra Magnus.)
I'm far more a fan of the Transformer toys and character designs than anything else, so - especially in the case of a line aimed at collectors [of Transformers and car models] - I'm only really interested in how good the figure is.
I'm unaware of a linking story behind Alternators (certainly haven't noticed it on the Euro packaging), so had assumed they were really just a stand alone toy line.
Still, I can easily see the frustration of there being two versions of the same character for people who like to imagine some sort of vaguely sensicle story behind the line!