Yup, should work as expected. If you’re interested in USB C ports, Vitaly made a custom expansion card which provides three external ports and one internal port. uHub Expansion Card
If I ever get time to design a new main board this is top of my list to fix. There are enough USB channels for both of those ports to have data. I don’t know what possessed them to go this way.
Not that I have any room what so ever to tell you what to do, but . . .
If you did ever get around to doing this, I seems to me it would make more sense to design one specifically to take advantage of a CM5, ala this thread: