It didn't ruin it, but it leapfrogged twenty years of history on Earth 1986-2006 that meant Target:2006 had to squash everything together and bring the future into the present to make it work. So Ultra Magnus is apparently new and shiny in 1986, but because Galvatron isn't created until 2006 he had to start there and come back.
I've said before that there is a rich vein of unwritten stories in a parallel universe where Galvatron isn't Megatron as his tech spec suggests, leaving scope for twenty years of adventures on Earth with them as leaders. What Season 2.5 of the cartoon would have been if Scramble City had been tacked onto the end of BOT. No Rodimus, just a rewritten Magnus who does have the balls to be a leader.
Having re-watched the Hate Plague - sorry Return Of Optimus Prime - recently (don't ask why) it got me wondering why all white Primes are not called 'Hate Plague Alloy Optimus Primes.' And was the decision to make Prime turn white in this story anything to do with there already being a white Optimus with the Magnus toy? Although the release of this on video here coincided with Powermaster Prime (bah!) in the US at the time of airing (1987?), there was still no Optimus Prime to buy.