IIRC Kega Fusion 3.54 had issues with the DAC speed and VGM initialization.
However, the current version, Fusion 3.64 seems fine and that's what I still use for MegaDrive logging.
All other emulators that feature VGM logging (Gens/GS, MAME) are worse.
There may be additional issues caused by bad start/loop/end points when trimming VGMs.
And there is VGMTool2 r5, which was used for trimming most VGMs on Project2612.
It does "trimming" by just removing any delays, so all YM2612 messages that were supposed to be trimmed off end up VGM sample 0. The more accurate cores really don't like that. (I patched the MAME/Genesis Plus GX core to be a bit nicer to P2612 VGMs.)
vgm_trim from vgmrips removes the YM2612 data that gets trimmed off, so even though it requires more care when finding the "start sample", it creates cleaner VGMs that also work a lot better with the newer sound emulators.