I find it interesting that in Magix SVPro 15, when you click on render options, it says use "Sony AVC/MVC" for highest quality....etc. for Internet. It doesn't say that for Magix AVC/AVC MP4. Could be an oversight when they redid the program, but why would I choose something that's less than the "highest quality?"
FWIW: I've been using x264vfw to render 3D side-by-side full, and 3D top/bottom full VR, videos. I write the video to an mp4 file and the audio to the avi file, then combine them using FFMPEG. The video is copied in FFMPEG, but the audio re-encoded.