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Regarding the ports, you pretty much summed it up. I would get rid of the HDMI but I guess some people would need them. Specially since DP 1.3 will be here later rather then sooner. But since AMD only has HDMI 1.4a for now as well I really don't know if it does any good.
Don't really count on a second SSD, much less M.2, they won't go for it.
HDMI does good because there are monitors with HDMI inputs on them. Apple isn't really in the monitor business, so the connections needed are largely not what appears on Apple's "monitor". If engaging a reference monitor that is a regular high end TV then HDMI is the norm. That's actually what people are going to see, not some mega bucks monitor that you get from a "pro only supplier" boutique supplier. Similarly, most modern projectors have HDMI inputs. HDMI is deployed in far larger numbers than miniDisplayPort and USB Type C. It is useful because it is what folks have available. The Mac only market is a bit skewed away from HDMI, but most likely even "Mac" people have some stuff with HDMI inputs on it.
Thinking about it, if Apple doesn't want to provision the second internal PCIe SSD then perhaps the SSD and one of the TB v2 controllers can just swap places.
x4 PCIe v3 TB v3 ; new "even faster" TB
x4 PCIe v3 new "even faster" SSD.
x4 PCIe v2 TB v2 (provisioned from PCH chipset).
The two x4 bundles from CPU don't need a switch so can easily be routed. Will need new route from PCH to I/O board on that connector though.
So can port configuration can go
4 Type A USB 3.0
2 TB v2 ( miniDisplayPort physical )
2 TB v3 ( USB Type C physical )
2 HDMI ( 1.4a or maybe 2.0 if get HDCP "big bag of hurt" sorted out)
same audio in/out.
4 legacy USB ports so folks won't complain need dongles for USB gear they already own. Keep them Type A so that start trend of Type C including TB on Macs ( the MacBook early 2014 will become a legacy oddball in the future ).
Aggregated TB bandwidth 40 + 20 = 60 . Previous Mac Pro 3 * 20 = 60 . So it is a minimally a wash, but at least haven't falling into backslider status. [ newer high I/O bandwidth RAID devices will be happier on the one TB v3 controller than old; so probably pragmatically incrementally better than current MP on total aggregate. ] Again have dongle-less compatibility for currently owned TB v1-v2 devices ( won't need new $30-40 cable to make them work ). 1-2 legacy Apple TB Display docking stations would just work. Likewise for folks with 2 miniDP monitors, they can hook-up without adapters (if don't have any TB v2 devices). Having TB v2 and TB v3 ports on the Mac Pro is somewhat like when Apple had FW 400 and 800 ports on the Mac Pro ( 2006-2008 and Mac G5 ).
For folks who "hate" TB and love USB there are 6 USB 3.0+ ports as the TB v3 controller independently provisions USB 3.0 gen 2. So a "new and better" on that front too.
2 HDMI in part so that don't have any "raw" miniDisplayPort sockets. ( Folks won't confuse them for TB v2 sockets ). If have 2-4 3rd party monitors more than likely at least two have a HDMI input port. Can hook up with hogging a TB port. The gap between DP v1.2a and HDMI 2.0 is basically firmware to do HDCP v2.2 AMD (and Apple ? as needs hooks in the core OS graphics stack) will probably fix that later. That is fine if the Mac Pro update is coming later also.
If they swap 2 mDP + HDMI for 2 HDMI ports then technically there should be be some "back panel" room for some digital only input (or output), but I doubt Apple is doing to do much past what is easily supported by Intel's chipset audio and consistent with the rest of the Mac line up. So the audio in/out will stay the same.
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