You are right, it is not possible to mirror MIDI-in to MIDI-out at the hardware level at the moment. It can be only configured to mirror MIDI-out to MIDI-thru, instead of MIDI-in to MIDI-thru (in the settings menu). But good idea, might be useful sometimes, I will add this for the next version.
But of course it is possible in software. Shouldn't be too difficult to patch Cynthcart to store each incoming byte to the output port. But might need a small ring buffer.
Cynthcart has released the source code, so should be easy to modify it:
I would guess would be about 10 lines of assembler code for the ring buffer. And I would use the send interrupt, to send the next byte of the buffer. A good assembler programmer can do this in 1-2 hours.
Note: Cynthcart is not "open source", but if you don't sell your modified Cynthcart version, no problem to use it on your C64. Or you could even send a PR to Paul for integrating it as a configuration feature in Cynthcart.