They're going to program it in Latin and NavahoMohicanDelawareish but not Klingon (as seen in TUC)?
Where would they have learned Klingon? The first two are Earth languages, well known to the Federation. In case of the latter, scholars are limited to phrases like "Prepare to be boarded!", and even those are no doubt more commonly delivered in the language of the victim, just to get the message across.
Kirk's ability to imitate a Romulan officer in "The Enterprise
Incident" is not particularly contradictory, as we later learn that (sorry, Diane Duane!) Romulans do not speak a language markedly different from Vulcan...
Also, the TOS universal translator is the size of a flashlight.
That would be the UT capable of deciphering new languages. The one merely storing known ones could be microscopic rather than "microphonic".
Besides, we didn't really see any actual TOS universal translators. We saw a gadget Spock built out of existing elements to serve the special needs of the day in "Metamorphosis", and an alien one provided by the Metrons. Starfleet-issue "external" UTs might well be the size seen in ENT or somewhat smaller, quite possibly integrated into the communicators.