This is a really interesting question. I still hope that we can mix the spoken languages in game with good subtitles. So we are able to hear in game Czech, German, Hungarian, Latin etc. when those languages should be spoken.
From my point of view the Czech-German tensions where more about policy (who should be Emperor / King of Germany, tax breaks and better promotion prospects for German people in the kingdom of Bohemia). So in this case the language shows more the cultural background and isn’t the real reason for the tensions. The different languages strengthen the tensions because a lot of people couldn’t talk to the other side properly (lost in translation).