I own UR44C and have spent some time by reverse engineering dspMixFx and its protocol.
I found that in Linux (as well as in Windows before installing Steinberg driver), sound card provides two midi input/output ports.
First ones connected to physical MIDI interfaces, but secondary connected to internal Yamaha mixer with DSP to control it.
After installing Steinberg driver the second midi ports became hidden, and only dspMixFx access to it (or access directly to usb endpoint).
I didn’t reversed all messages, moreover I didn’t chacked on new firmware 3.0, but on 2.x firmware I recognized the next.
It uses SYSEX messages with Yamaha vendor ID. I found 3 most important messages for update parameter, query parameter and receive parameter value.
Probably full midi implementation chart could be requested from Yamaha, of found in owner’s manual for some similar products like mixers, etc. At least earlier Yamaha published very detail information for their SYSEX parameters and codes.