How to force VLC to play a video fullscreen at a specific size?

Your question made me curious all day. I've been playing around on an Ubuntu VM for the past hour and did a little digging.

The first two set of options you are using:

cvlc --fullscreen --vout glx --no-autoscale --scale 0.65 video.mp4

and

cvlc --fullscreen --vout glx --width 800 --height 519 video.mp4

are targeting window scaling. If you remove --fullscreen from your command, you will see that the window opening is the exact size as you specify, but once you enable fullscreen, the video plays in the original size.

I have tried every single option that includes the word width/height in the official VLC command-line help and the result is the same.

Your third command is your best case. The third command is the only one that affects the video stream and not the window. So you have to find the best percentage that will play your video exactly as you want to.

The suggestions I made in the comments for Devilspie2 and kpie are affecting the size of the window as well, so they may not seem appropriate in your case.

Right now, your best shot is to find the ideal number for the --zoom option

Zoom will not give you the exact size that you are looking for since there is no way to specify width and height with --zoom. If you are willing to give transcoding a shot, then you might get the expected results