The only continuity in the G1 cartoon is "sell this toy this week".
Prime's internals get x-rayed in "A Prime Problem" and there isn't a hint of the Matrix. Fast Forward 12 months and all of a sudden we're expected to believe this uber-awesome cosmic megabomb has been part of Prime all along. He doesn't even get upgraded like Rodimus does when he takes ownership. Prime's just... Prime, just as Alpha built him in "War Dawn".
Prime also addresses Trailbreaker as Trailblazer and Spike as Splick in A Prime Problem.