Matlab assumes and always display the video with a pixel aspect ratio of 1:1.
My guess is that your original video specify a different aspect ratio, that VLC respects (hence it stretches the video horizontally). Unfortunaly, that property is not accessible within matlab. The MP4 format is sufficiently complex that extracting that information within matlab without the help of a library would be substantial work.
So, if you want to process that video in matlab, you'll be stuck with a final video with a 1:1 pixel aspect ratio. It must be noted that the video is not constrained. It's more that the original is artificially stretched from its actual 720 pixels width by VLC.
A quick search shows that a command line program mp4box would allow you to change the pixel aspect ratio (without recoding the video). See this page where it's discuss. Never having used it (or heard of it before today) I can't vouch for it.
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