Access to rPi onboard I/O header

Hello, I use a very old Linux based box for test drivers, it provides multiple buffered DIO to convenient screw terminals on the case. I want to replace it with something modern, and looking at rPi. However, access to the (unbuffered) pin header on the CPU board looks untidy, none of the cases I’ve looked at clearly support it.

I can lash up some buffering, and at a pinch install the Pi in a larger case, but would be interested in any suggestions on what might be doable while still using the housings provided. An alternative might be a DIO board with USB interface if one exists – but there needs to be a convenient way of interfacing the USB to my (C++) software.

Any suggestions welcome.