I sincerely doubt interconnects are going to be the problem the OP thinks they will. First of all, individual connectors have not changed much in size, but the serial data-rate we can push through copper connections continues to rise. Fiber optical connections are already used to implement PCIe in many applications (Thunderbolt is, in part, a fiber optical PCIe link).

One huge advantage of fiber optics over copper is that you can send many data streams down a single fiber using different wavelengths and/or optical modes. This is why backbone fiber bandwidth keeps growing even over fiber links that haven't been upgraded. It's a function of what you hook up to the ends of the fiber, not the fiber itself. There is tremendous room for bandwidth growth in optical fiber.

Apple definitely doesn't need to use non-standard interconnects for the new mac pros just like they didn't need to use custom connectors for SSD's in their laptops. They just wanted to.