Also a good chance to fix the intro logo sequence synchronization with the music.
I am unsure about which synchronozation you are talking about. Synchronization has been one of the major issues with version 1.0 and had to be reworked for version 1.1. I'll attempt to do my best for version 2.0.
Vanilla FF6A has slowdown
Yes, just like vanilla FF5a. I can only fix those who are introduced because the CPU time exceeds the time that is available in one video frame, I cannot fix other slow down effects due to bad programming, those are especially present in FF4a but also in FF5a, I am not sure if any are present in FF6a.
I don't know whether his FF6 hack does the same
Version 1.0 and 1.1 uses a mono version of the original Nintendo sound mixer, but uses a higher sample rate, so overall it takes about the same CPU time than the original FF6a, that is between 25-40% of the CPU for the music engine.
Version 2.0 will use the same variant of sound mixer used in the latest FF4a and FF5a patches which will greatly reduce CPU consumption, to 15-25% of CPU time.
It is very difficult to predict how much slow down this will actually fix, but very likely it'll fix at least some of them, like my FF5a patch does. The time the sound engine takes is extremely variable, as it depends on the # of active sound channels, the frequency of the samples being played, the length of the loop points of the said samples and the reverb parameters among other things. That is why the CPU usage of the sound engine is so volatile and variable.