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DVDs don't use square pixels so the resizing is normal when playing DVDs, only players might only report the resolution, not the aspect ratio. I don't know what VLC reports. MPC-HC shows both like this: 720x480 (16:9).
When you encode using Handbrake with the Anamorphic option set to anything but "none", Handbrake will set the resizing to be done on playback as per your example. With Anamorphic set to "none" it'll resize to square pixels when encodong, so the display aspect ratio and the resolution will be the same. Keep in mind though, not all hardware players support anamorphic MKV/MP4 files, so make sure your player displays them correctly before using anamorphic encoding, otherwise disable it and resize to square pixels.
I've never used AviDemux either so I can't help there, but most GUIs which can set aspect ratios on playback have an "anamorphic" option. Or look for something like "keep aspect ratio". Assuming AviDexmux can encode that way..... I'd guess it can but some older GUIs always resize to square pixels, or the anamorphic option may only be available for certain output formats.
Well it looks like Avidemux makes you calculate the pixel aspect ratio using the resolution and display aspect ratio, then enter it manually. Assuming this is up to date. Scroll down to Pixel Aspect Ratio. http://www.avidemux.org/admWiki/doku.php?id=tutorial:h.264