You are right, the timing is minimally different but generally MAME is the best emulator and very close to the real hardware.
MAME is not perfect (e.g. Raster effects) but if it works in MAME then you can be sure that 99.9% of the time it will work on real hardware - no matter if MVS, AES or NGCD.
The only thing you should keep in mind - ALWAYS use the original bios, the UNIBIOS falsifies some things (e.g. the timing).