You could tackle this a few different ways.
1. A little bit of homebrew never hurt
Dependent on how, "dependent" you want to be on the core rulebook, you could homebrew, and say something like "once your character hears the language and context with it, he immediately grasps it and can speak and comprehend it."
2. Roll d20
You can see if you can roll a d20 adding any relevant modifiers to see if you can comprehend the language. Since its obscure.
Just no, if you feel its broken, then don't utilize it. maybe in your universe some languages are impossible to comprehend. maybe polyglot only applies to basic languages. So if you want some languages to be mysterious to you to help your experience, use this option.
All in all, I would say go with your gut feeling, remember, role-playing games are about fun and imagination, and if there are rules that could hinder that for you, you should bring that up to your game-master in order to rectify it. If you aren't having fun, you might as well not pray at all.