Would it make sense to introduce a name:translit tag for transliterated names and let mkgmap choose one of them, e.g., mkgmap --name-tag-list=name:en,int_name,name:translit,name or (for native users) just mkgmap --name-tag-list=name:translit,name? The transliteration could be implemented as a separate preprocessing step or integrated in mkgmap so that it can be executed on the fly, when a substitution of name:translit is requested.

ISO 15924 and IANA define some language subcodes, such as sr-Cyrl and sr-Latn for Serbian written in Cyrillic or Latin, but I did not find any subcode for transliterated Russian or Greek, for instance. We could of course invent such codes ourselves, but it could be controversial to add, say, name:gr-Latn and name:ru-Latn to each Greek or Russian location in the OpenStreetMap database. (It could provoke edit wars, because not everyone is following the current version of ISO 9.)