It should not be too hard to add support for theory and logic definitions.
Two options:

1. add callbacks for "fake" commands: (theory ..) and (logic ..)
2. modify the Pomelo parser to be multimodal. This can be done by accepting a first token Mode(m) that sets the mode. (EDIT: not needed)

https://smtlib.cs.uiowa.edu/papers/smt-lib-reference-v2.6-r2017-07-18.pdf