What Apple did was screw over it's loyal users by forcing a switch that didn't really need to happen.
They also dumped SCSI? Was that a "proprietary" port too?
That's kind of like the problem with Thunderbolt. If you are lucky enough to have kit new enough to have a TB port, you can't use any of that new gear to connect to anything else. That includes Macs as well as PCs. Having a PCIe slot doesn't matter either as you can't get a TB interface on one of those.
Apple is great at forcing ugly, expensive, and unecessary transitions.