I posted this awhile ago, and kind of forgot about it tbh.
However, I finally figured out what RSO was talking about when it says that ground-water wasn't configured; it's because with this mod active, RSO only looks at the omnimatter resource configuration, and, since it doesn't include ground-water or lithia-water, throws this error because it doesn't know how to handle spawning the ground/lithia water patches (since they are only defined in the bobores resource config).
Manually adding the ground-water and lithia-water spawn configurations to the omnimatter file once again allows Ground Water and Lithia Water to spawn, and no longer causes this message to appear.