I'm using a version of RFTools built off of the current github (2.53) and I was looking through the ore dimlets, and found that there were quite a few dimlets made from ores that were basically useless for my pack.

I looked into the dimlets.cfg, and found that those dimlets did not appear there. I know that they can be disabled via dimlets.json, but it would be beneficial to be able to disable them via the dimlets.cfg like other dimlets.

You can actually do that. You can still put <...>.id = -1 in the knowndimlets section of the config. You just have to find the name. An easy way for that is to dump all dimlets in game: /rftdim dumprarity

Oh, thanks!