So, I like the automatic mod compatibility this offers, it's rather nice. However, there are some modded ores I personally have run into that I don't want deep patches popping up for, such as peat from Lignumis. As far as I can tell, currently there's no way to turn this off.
However, there are other modded ores that I would want ore patches for, and I could see scenarios where one that wouldn't make much sense for ore patches and one that would are present in the same mod. Thus, using the same system that's used to detect those ores and generate compatibility recipes and patches for them, it would be nice to have an option generated per-ore to turn those recipes and the generation of patches for a given ore off.

Hello, late reply sorry but indeed some modded ore may or may not make sense to have deep core ores.
Yes this should be possible to automatically generate ore configuration to toggle them on/off (it would be a startup setting that would require restarting the game on change). It would be a bit laborious to do.
Currently it's possible to ignore or use the manual tool to remove the orepatches.