I think a lot of what you are thinking to be CDI limitations might be more in the exhaust.
Expresses do the same thing and its because the exhaust is just so tiny and baffled.
There is a CDI rev limiter for sure, but I think what you are looking at here is an exhaust issue.
Expresses do the same thing where they will be running fine then you go down a hill and they four stroke like HARD right at the same speed every time. Its actually just the fact that the exhaust is so small and baffled that it stroked out at the same speed every time.
I have only worked on a couple QT50s and one towny, so I am not an expert. Fersher try different CDI boxes and such to see what happens.
At the same time I would also buy like a pocket bike pipe and a spare stock pipe to fab up a more free flowing expansion exhaust.
Both would be pretty cheap experiments.
Also I have a YT60 CDI and a towny CDI here I think. I will try those.
Maybe you should look at CDIs for PW50s. PW50s are pretty much the same engine as QT50s. I don't know too much about the electrics on a PW50, but they don't have lights so its possible that they are 6v like qts. Maybe not though.
Also I know some razz stuff works on QTs. I used an ignition coil off of a razz to make a QT run. I think that would be a really easy way to turn a QT50 into a 12v system, just take all the electrics off of a razz.