Wow, very impressive build. And nice to see Pybricks mentioned. How are you planning to control the two hubs and do they communicate with each other?
This has been driving me crazy as well, I commented on it in the thread below as well. So far I only one (!) out of seven Z60 turntables that I own runs perfectly fine. Two mesh really badly with the 12T gear and the others are just not great either but okay-ish, sort of like what you describe.
I am trying to figure out if this is a problem in older or newer sets. The thing is that 42042 is a set from 2015, and that uses a similar set up as yours. And I would assume it meshed fine back then. The Z60 beveled turntable gear was in sets between 2015 and 2021.