I’m likely missing the whole point here, but I have kibitzing on both sides of my family. Why not use the Import/Export facility on a machine configured as you want, to create the update files containing the custom configuration? Then use your installer or a batch file to run each user copy of Multi-Edit using the /R command-line flag to run the update macro? (On a side note, the documentation for the update facility is under the heading Adding Features to Multi-Edit in the online help.) Of course, as Michal noted, macros run that way execute before the program is fully initialized; whether that would be a problem for a macro only attempting to update the command map, I don’t know.
More versatile, albeit more involved methods would use either Multi-Edit’s DDE or COM server to do pretty much the same thing. The documentation for that is in the section right after the update reference, titled Integrating External Applications. Overkill, perhaps, but not all that hard to do, if you’re even a little familiar with either interface. Besides, it’s useful to know for other things, as you can pretty much totally automate Multi-Edit that way, especially using the COM interface.
I guess them’s my 0.02 Zorkmids.