Personally (and purely personal opinion) I don't take benchmarks for Inventor seriously from somewhere like Tom's Hardware, unless there's someone behind that work with some credibility and significant experience with this software, it's too specialised and isn't comparable to gaming benchmarks, so I wouldn't recognise the results as being definitive and legit as I wouldn't know for sure that it was done in the right way with consistent and reliable data sets.
But yea I've got a fair bit of experience and history with AMD. Before I mention more though, FYI Inventor doesn't support dual or SLI cards the same way in that it doesn't support dual Xeons. So for your dual Quadro system, one of those cards is doing literally nothing for Inventor, which is why you see zero scaling with performance on that system. I sincerely hope you weren't sold the system on the advice that the two cards would benefit Inventor, because they most certainly do not.
Comparing the two identical systems, 1 point can be within normal variance and likely isn't anything to do with the GPU. You could lose a point purely through a keen background process existing on one system but not another, taking minimal CPU resource causing the tests to run ever so slightly slower, I think in real terms you're not likely to notice any real world differences between 2 systems with a 1 point variance. Can you do a 5 or 10 cycle test on both systems and post the results here?
Regarding AMD though, they've had a choppy history with Autodesk, at one point in the past (a long time ago) Showcase just didn't run at all on AMD cards and Inventor had all sorts of graphical issues. AMD also never had as good of a driver release schedule as NVIDIA, the NVIDIA team release drivers on a regular basis whereas AMD could go several months sometimes longer without any software optimised drivers.
Regarding the actual hardware, AMD are widely considered to be second best and are openly happy to admit they cannot compete with NVIDIA at the top end of the market. For example with this generation of gaming cards, AMD have absolutely nothing to compete with even the GTX1070 which is the current third tier card from NVIDIA after the Titan X and GTX1080. So AMD with their current generation of cards are way behind NVIDIA.
It's kind of a different story for 3D CAD though. I personally own a FirePro W9100 and a Radeon RX 380 from AMD, and from NVIDIA a GTX1070, GTX970, Quadro M4000 and a Quadro 2000. In terms of real world performance, they're all pretty much identical under light load except for the Quadro 2000 which is too old to cope. On the bench test, again all the cards bar the Quadro 2000 push out the same performance. Variations will begin to occur when the system hits VRAM limits on each card, the W9100 has 16GB of VRAM whereas the RX 380 has 2GB and the GTX970 has 3.5-4GB. Another thing I noted with AMD is that their FirePro cards run extremely hot, it didn't take much for the W9100 to hit 92 degrees causing the awful reference blower fan to scream like a jet engine, causing some thermal throttling on the core clock.
Soz for the long reply, the short answer is that as of today I would choose NVIDIA over AMD. However AMD are soon going to be releasing their Radeon Pro cards which replace and supersede FirePro, so it remains to be seen what they'll be like with respect to actual performance and driver support for Autodesk software.
