Copying primary language translations to region subtag
The general question has been resolved, not clear whether there are specific issues at hand.
Should translations for 'en' be copied to 'en-gb', 'en-ca', 'en-au', etc even if the message does not need to be modified to suit the region? IMO this is silly, but people are doing it, so it would be great if the wiki prevented saving identical translations in subtag'd languages.
In general, this is not necessarily wrong: there might be some applications which don't handle language fallbacks. In the "MediaWiki" namespace saving an identical message is (still?) prevented, but by MediaWiki core itself rather than Translate (perhaps only for locally installed messages?).
In general it should be possible to add a checker warning translators about the identical messages; usually best done by someone with intimate knowledge of the group/project.