Three possible reasons:
1.) Hasbro Had little to nothing to do with these series and Takara Tomy working on them. the same thing happened With the PS2 game "Transformers: Tataki (or Call of the Future.)
2.)Optimus Prime supposedly dies in the Headnmaster series, and many American fans were distraught by his death in the movie leading to his revival.
3.) a happier ending might have been wanted in America. In America , the war ends, the Autobots win, and Cybertron goes into the second golden age. in Japan however, this lasts a short time with the Decepticons returning, and reducing Cybertron returning to an energy-less planet, The Matrix losing all of it's energy and wisdom helps with this, plus Ultra magnus supposedly dies by Sixshot (who would have had a secret 7th transformation), Rodimus would have left and if memory serves correctly fortress Maximus would lead the Autobot(its possible that Scorponok would lead the decepticons with this).
Sorry if this focused to much on headmasters. But I think the some episodes of Headmasters are on Youtube.