Make your choice based on the features that you need overall, ease of working, user-friendliness (if that is possible in an nle) and stability.
In VPX, track 1 is the bottom of the pile, whereas in Vegas it is on the top. Take note of my other post about the features and in particular the difference in the way that tracks are handled. So we should not expect that transitions are superior in terms of quality both products. All the MVC encoder in the price class of both tools are limited in the data rate due to licence costs. My impresson at the time of testing was that render quality was quite similar. In terms of render quality - well, since I have not tested the latest version of VPX that is hard to assess too. My tests were some time ago, so I cannot assess how the number of crashes are in the today versions. Overall, the s3D interface in Vegas Pro had a better logic in my eyes, compared to the tools of VPX (everything can be done in the s3D interface in Vegas, for VPX it was necessary to switch between menus). The keyframing was better, the autocroping after the stereoscopic adjustment were better.
When I tested Vegas Pro versus VPX for s3D reasons, I came to the conclusion that Vegas is more superior in terms of s3D. Which tool has the lower number of bugs? (crashes etc.) It seems that the 3D (stereoscopic) transitions are better in Magix Video Pro X. Which tool is best to create 3D stereoscopic slideshows (to generate an MVC file 2 X 1920X1080, frame sequential)? Vegas Pro or Magix Video Pro X?