Top Guns were originally designed to run TRS/speedmaster drives, both of which obviously use a transmission. When Bravo's came out, the initial transfer didn't work as well, because without the transmission, the boat porposed quite a bit.
Props weren't where they are today, so the problem wasn't easily corrected in the following years without having to do a fairly significant amount of re-rigging.
These days you can prop those boats to eliminate much of the imbalance, without having to do a major refit. The years that SOME BOATS had imbalance issues, were typically 1993-1996. I had a girlfriend that had a 1995 Top Gun with bravos', 500's, and was the worst running Cigarette I've driven. Another friend bought a 96, that had 600's & Bravo's, which had its' share of balance issues as well.
These are just two examples, which does not mean that there weren't great boats built during those years. The main thing to pay attention to, are the years that the Bravo drive was simply rigged to a TRS balanced Top Gun.