Both. Top ports are really for temporary connections. Having two TB3 and two USB 3.1 on the rear is inadequate. It's unusual for any desktop box to have four total ports on the rear by default.
Bear in mind that every pair of Thunderbolt ports is a bunch (4?) of PCIe lanes committed - and the whole point of this MP is customisability. The MP has a ludicrous number of PCIe slots - even more than most PC desktop workstation - which can be used to add whatever connectivity you need (Fibre channel, 100Gb Ethernet, more USB A/C) - and other types of hardware (extra GPUs, specialist audio/video interfaces, storage) would be fitted internally as PCIe cards anyway.
On top of that - the base model has 4 x DisplayPort and 2 x HDMI, plus the VegaII MPX modules each add
4 TB3 ports, - any other MPX GPUs that appear will likely follow suit - so you're not going to be relying on the built-in TB3 ports for connecting displays (not that you'll want to once DP2.0 cards and displays start appearing, if Intel takes as long adding it to Thunderbolt as they did with DP1.4).
What I
don't like is the idea of top-mounted ports on a machine that will often live
under a desk. Seems to be the worst of both worlds c.f. front-mounted (for easy access) or rear-mounted (for tucking cables out of sight). Well, that and the way Apple couldn't contrive to make a $3k-$4k expandable desktop for those who need 0 < n < 8 PCIe slots and < 1TB RAM or - failing that - at least make the $6k machine substantially more powerful than the $5k iMP. Apart from that (Mrs Lincoln) I think the MPX concept is quite neat.
T2 is near useless. It locks in a proprietary SSD tech that is hugely over priced and slow. Almost any NVMe SSD is orders of magnitude cheaper, and is significantly faster.
...but at least with the Mac Pro you should be able to chuck in a PCIe-to-M.2 card to expand the internal storage
and there's space & connectors for spinning rust (or cheap SATA SSDs) for bulk storage. Pegasus have already announced both a RAID module that goes in a MPX bay and a dual SATA cradle that goes at the top above the SATA/USB/power sockets.
The real problem with the built-in SSD is that the entry level 256GB is uneccessarily small for a system disc that will be used for pro applications and their temporary files.
The 10GbE ports are probably on the motherboard.
Nope - it says quite clearly on the Mac Pro tech specs page on apple.com that the PCIe I/O card contains 2 x TB3, 2 x 10GbE and 2xUSB 3.