It seems like we have very different experiences – strange, I will check that again when I find the time…
Cubase is special as you cannot disable or enable ports. If you don’t use a port in any tracks the port will be disabled automatically.
I am using a MOTU Midiexpress 128. This one has definitely multi-client drivers as Ctrlr standalone and MIDIOx and any tested DAW does work in parallel. But within Cubase I cannot select the same port in Ctrlr if it is already used by Cubase. The same thing with Reaper and with Ableton Live 9. Also the same thing on my virtual Mac and Ableton Live 9.
in Reaper the Ctrlr plugin does work almost perfect: NO selection of any ports needed! In other words, you leave the Ctrlr midi input and output device selection BLANK. Just enable input from host and output to host and set the thru setting to host to host.