Hi telecastle,
I've read a few reports that USB passthrough is broken on ESXi 5.1, but I have not personally investigated that. I believe that passing through USB controllers is not something we officially support (to the best of my knowledge, which I readily admit is not necessarily complete), and passing through motherboard-integrated devices is fraught with peril, so I would not be surprised if it didn't work...
Regarding the number of ports and controllers: In general, the designers of the hardware platform can do whatever they want in terms of mapping physical ports or functions to USB controllers. There are no definite rules, and often it is not documented anywhere, and you just have to figure it out for yourself.
In the case of my Macmini6,2 here, some experimentation with System Profiler tells me that:
00:1a.0 is the controller managing the four rear USB ports when USB 2.0 devices are attached.
00:1d.0 is the controller managing the internal USB 2.0 devices: an IR Receiver and a Bluetooth USB Host Controller.
System Profiler also reports an xHCI (USB 3) controller at 00:14.0, which also manages the four rear USB ports when USB 1.x or USB 3.0 devices are attached.
In other words, if you attach a USB 1.x or USB 3.0 device to any rear port, it'll appear on 00:14.0; If you attach a USB 2.0 device to the very same port, it'll appear on 00:1a.0. I don't think you can attach any external device to 00:1d.0 without opening the Mac Mini and perhaps doing some soldering or rewiring. 
Cheers,
--
Darius