I'm not sure Mame64 can do what you want.
The most popular MAME derivatives that support Command.dat include the following:
MAME Plus!
MAME Plus! UI
MAME Plus! eXTended
MAME Plus! Plus Kaillera
MEWUI
M+GUI
ShmupMAME
ShmupMAME UI
ShmupMAME+GUI
I'm running MamePlus! and really like it. If this feature is important (and I can easily see how it would be), you might consider switching to MAME Plus!