Each character starts out with as many Language Slots as their Sagacity score. More Slots can be acquired via the Polyglot Feature. If Sagacity is permanently improved, additional Slots become available.
The first Slot is always filled with the mother tongue of his Homeland. Any additional languages are up to the player and always cost one Slot.
Slots can be left unused until they are filled during play, either through a learning effort or retroactively, as long as it can be plausibly explained.
Characters are fluent in all languages they paid Slots for, although they can pass as natives only in their mother tongue (with exceptions explainable by background). In addition, depending on how close a target language is to a language they already know, they may be able to understand parts or even most of it without spending Slots (but not actively speak it).
Most game settings only have a few (often racial) languages, with a common trade tongue to bind them all together. That is not the case with Auropia, a high medieval inspired setting.
Imagine the language complexity of the modern world, exacerbated by a lack of standardization and public schools. Every region has its dialect continuum of languages, harder to understand the farther you travel. If there is such a thing as a lingua franca, it exists in the scholastic sphere, differing from religion to religion, and sometimes period to period.