This mod has a strange problem with omnimatter: the 'sort raw ores' recipe becomes free instead of disabled.
With bobangels only, this recipe is disabled and replaced by angel recipes, which is as expected.
I'm using the modpack named AngelBob, and all the involved mods are updated to most recent. Omnimatter is also most recent version.
However I can't get bobangel to generate the starting patch properly, so I installed omnimatter.
With omnimatter, this recipe is magically brought back, and costing nothing at all, and takes 1s to craft.
I think this is caused by omnimatter removing the relevant ore, causing some error in bobs mod.
The ingame GUI says this recipe belongs to bobs library, so I'm posting this bug report here.

I disabled the startup setting 'Enable recipe ingredients cleanup', and tried again. The game couldn't even start.
It seems this mod combination (BA+omni) cause this recipe to require raw gem ore, which is deleted by omni and becomes invalid.
With this setting, the only item input of this recipe is invalid and then removed, so this recipe becomes free.
It seems there is something wrong on the omni side, but I can't contact omni mod's author, discussion is disabled for that mod.

I've posted this on the Omni discord. Asked the Omni devs to have a look.

I've been told that this has already been fixed, ready for the next version of Omni! 🙂

That cleanup script is purely a compatability thing. It makes it so the game will load when otherwise it wouldn't, but doesn't guarantee everything works correctly.
This isn't exactly the target use case of the script, but good to see it's doing it's job.