Xeon E5v4 are confirmed to be available on March/April.I didn't realize the Skylake Xeon's with 48 lane PCIE weren't shipping until 2017. This leaves TB3 as very doubtful in my mind for the MacPro 7,1.
As you say, the only CPU's Apple is left with are the 1600 and the 2600 Broadwell-ep with 40 lanes and that still uses the C610 chipset with 8 PCIE 2.0 Lanes, so in order to get Thunderbolt 3 they need to come up with 8 more PCIE lanes.
1. Intel could build Apple a custom chipset with 16 PCIE lanes
2. Apple could cut the link speed of the second GFX card to 8x
3. Apple could use 2 1600 CPU's and only offer TB3 on the high end MP7,1
1 is the best case, 2 is the wisest move, the second GFX card doesn't do anything most of the time and we're still talking about and 8x link at PCIE 3.0 speeds. 3, I'm not even sure if the 1600 supports SMP or Apple could even fit 2 of them in the nMP case even if they did.
None of the above are very likely, what is likely is we'll see a refresh of the MacPro at WWDC 2016 in June /without TB3.
Tb3 also is confirmed by leaks on OSX beta,
Tb3 runs on Pcie 3 (2/4 lines) "in a tipical implementation wired to the cpu root complex not the PCH" tipical here means not the unique way to wire it.
https://thunderbolttechnology.net/
It's more likely a custom c610 to be released for tb3 but not the only choice.
Haswell-EP on C610 leaves 40pcie 3 lines, from those Apple could take 4 pcie 3 lines for 2 tb3 headers and have 4 available for 1/2x NVMe, or take all 8 for 4 tb3 headers.
I'm speculating, I think at some point Intel should announce either a custom x99/c610 "tuned" for tb3.
At the moment osx beta leaks, point to 4 tb3 ports (2 headers), and 6 tb2 ports or usb3 (using the PCH).