It ignores it...sort of. Its a direct continuation of the original Marvel series...but moving things on 20 years for no good reason. If you're doing a retro book, you might as well pick it up from exactly where you left off, you'll be preaching to the converted with this thing anyway. Personally, if I were embarking on this, I'd have gone back to #80, what with #81 being a bit of a rushed conclusion. It's not something I personally felt was a necessary project to embark on.
As Generation 2 is one of the best Transformers comics out there, it's a shame that revisionism on the part of the publisher and author will make this an irrelevance now. Furman has reportedly said that he doesn't particularly care for Generation 2 and is actually embarrassed by it as being "too nineties", a pity given the high regard that comic is generally held in.