I agree that "Dungeon" as an in-universe term is probably best replaced by something like a "Trial".
That way you divide the metagame concept of a dungeon with the in-universe idea.

If you still want to call it Dungeons, how about have a history of it in your setting. Such as:
There's always been people who either like to explore or like (or have to) fight monsters who accost civilization. Over time, those became known as adventurers and the locations where monsters generally dwell as dungeons. Over time (or rather quickly by divine revelation), it became clear that some dungeons were made by the Gods (or at least some ancient being of power) as a way of cultivating and harvesting power. In time, linguistic patterns shifted and place of power such as that became known as Dungeons. So while 'dungeon' can refer to most any dangerous place or ruin, it generally refers to places made via the architectural magic to be a proper Dungeon.

That way the in-universe language the characters use is in synch with the out-of-character terminology.