[BUG] x264 colormatrix option changes when "Overwrite input type scan" is enabled

[Selur]

is the standard for ISO/IEC MPEG (which is what DVD uses)

not so sure about that,..
DVD often has special rules that differ from normal MPEG containers, which is why repacking into mpeg often isn't the brightest idea.
see also: http://avisynth.nl/index.php/Colorimetry#DVD.2FMPEG-2

So I guess my question is, if a DVD doesn't have any color space tags, should it be assumed to be 601, or 709?

Nope, DVDs have no color space tags at least none MediaInfo/MPlayer/FFmpeg know of and report.

-> looking into checking out what changes on the reload,..