zmatt: I would not worry about the design, I'm guessing at least 90 % would be stationary use.
rv6502-2: I don't see the use for the first two options but the third would be rad!
Of course copying to or from SD or eMMC will not be better than the USB 3 port but what if in my case I often copy from one HDD to another or to a USB stick? Also, I can still make full use of my external eSATA drive that way, which otherwise only has Firewire or USB 2 available. Not really hard to understand the advantage this gives.
The SoC of the Raspberry Pi 3 does not have the same cores as the Pyra. Benchmarks suggest they are about even in multi-threading.
hns: Coincidentally, mine is also a WD 1 TB drive but with external housing. ;-)