I've done some research and now understand that the MPD compilation that Moode OS uses does not enable FFmpeg as a filter, but only as a decoder. This is a compile-time option and that decision resides with the developers, and probably for good reason. (likely just not needed)

I've figured out that Moode OS's interface for CamillaDSP allows me to setup a lowpass filter for the subwoofer, and it was actually straight forward. There's even a guide on how to do this that I found through their forums.