I think you need to look up the word 'proprietary'... I would bet that those 300 pin connectors are Molex HD Mezz or something similar. Just because it's not a connector you normally see on the outside of a personal computer, it doesn't mean that Apple has made a custom one. The Mac Pro will not be sold in huge numbers - making custom shape PCBs is simple, tooling up to make custom board interconnects is not and is probably not worth it (even for Apple) at these volumes. Get a magnifying glass out, look at the connector and I'm sure you'll see some branding on there that will lead you to the manufacturer.

As Dennis Murphy says, they look like connectors that have been used before.

@gsf I agree!

I know ifixit hasn't been around that long, and they like to write sensationalist copy about the "right" to repair, but you'd think they'd learn a little about the subject.

The microcontrollers on the inside of the port panel must be for the illumination that lights up the ports. Somewhere there's a sensor that knows when you're turning the thing around too. Do they use a MEMS sensor for that?