Is there any reason to think that ripping and encoding in one step produces better quality files than ripping a bunch and then encoding them over night?

Ripping and encoding is always two separate steps.

Your particular software might appear to do them as a single step, but that's only because it's hiding what's going on under the hood. The sofware doing the ripping is a different piece of software than what's doing the encoding. Even if the encoder software is a realtime .DLL or codec, it's still separate.

The only difference between the one-step/two-step arrangement is timing and convenience, it has nothing to do with the quality of the resulting files.