For Zymkey 4i, the intended use case is for customers to connect to the perimeter circuits using a microUSB cable plugged directly into the microUSB connector on Zymkey 4i, per the instructions here
Some customers have done as you have suggested, and soldered the wires of USB cable directly to the four holes on the protokit PCB. This allows them to patch out the signals and experiment with different types of perimeter circuit design: some use switches, others a custom PCB on the lid, others an external (to the enclosure) perimeter circuit.
Would it be helpful if we offered a perimeter detect lid ? so that you did not need to design you own ?