The word chimera for example. When encountered for the first time in a book, it comes with a description of the beast. There is however no help on its pronunciation. So in your mind, you may pronounce it the same way the start the word cheese. Is there a word for this situation?
Learn English – word for knowing the definition, but not the pronunciation of a word
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The OED gives ay - pr - eye - 'or - eye as the only pronunciation. I (an American English speaker) usually say ah - pr - ee - 'or - ee (which appears in the MW pronunciation you cited), but I hear both. As for Immanuel Kant, he would have likely pronounced it differently than an ancient Roman anyhow. One of the key differences between classical and ecclesiastical Latin (the latter of which Kant certainly would have learned) is pronunciation. So, it's hard to say which one would be more "Latin" (neither is spot on).
The Wikipedia article on the topic simply refers to these as irregularities, though one might also call them idiosyncrasies or anomalies - though none of those terms refer specifically to words with unusual spelling / pronunciation.
I think the best word to describe such irregularities is aphonetic, though that word seems relatively rare. I didn't find it listed in any dictionary, but here's an example from one of the documents in that Ngram search:
Best Answer
Such a word is part of your
and your