2. Is there any reason to expect a difference with NVMe?
If doubling [roughly] the speed from 250Mb/s to 500Mb/s on PCIe does absolutely nothing in terms of performance, I would think that "tripling" this with an NVMe would be a very expensive way to get the exact same results (I am guessing the best I could get from NVMe on PCIe 2.0 would be ~1500Mb/s with the Sonnet M.2 4x4 PCIe card; and 3 x 0 improvement is still 0!). But I do not know enough about computer hardware to know if this is correct. Perhaps the NVMe would indeed be faster for some other reason? Perhaps there is only a difference in speed with presets/project files that are significantly larger (2, 5, 10, 100Gb)?
3. Is this an inherent limitation of the Mac Pro? Or, what is the fastest possible configuration?
I sent the same questions to the software manufacturers to see if they have any insights, but I suspect this has something to do with SSD hardware, QD, bus architecture, or maybe 5,1 firmware. Or maybe it is inherent to how sample data is read from an SSD? Compression/decompression? My system is as up to date as possible without getting a Metal GPU and installing Mojave (or just updating firmware and going back to stock 5770 GPU and High Sierra), but not sure if this would change anything.
Not Mac specific, but...
Linus tech tips did a blind test with a bunch of SSD equipped PCs for general system responsiveness, app loads, etc.
Most of the staff picked the SATA3 connected SSD as the most responsive machine or couldn't tell the difference.
The test included a 3.2GB/sec NVME drive.
Which matches what I've personally found as well. I've got 4 SSDs in my Linux desktop - 3 SATA (mix of 850 and 860 EVOs) and one NVME (970 EVO) and unless you're doing a flat file copy they all perform pretty identically almost all the time.
For the vast majority of tasks, SSD is not the bottleneck at the moment, it is software optimised for slower storage, cpu throughput, etc.
Not saying there aren't edge cases where faster SSDs will be faster, but if people are expecting night and day performance from a faster SSD vs. a regular commonplace SATA connected one... you just aren't going to see it 99% of the time you're using it.