Those are probably a consequence of beveling the edge, the messy geometry comes out for free. You can always try it out on simpler geometry as a test, so you can start noticing how it behaves.
Thank you for your suggestion. I went with a boolean cutout for now, not sure how it will turn out at the end, but the shading looks cleaner.
If it doesn't end up how you want, remember it's always the best idea to start over.
