Save size of track as default?

Why not just open up the theme config and find the layout height ? It is not as much work as you may think and will stand you in good stead for further mods down the road ;)

In WinXP it's the ColorThemes folder under \Documents and Settings\user\Application Data\REAPER\. Rename the correct ReaperThemeZip as ReaperTheme.Zip, open the package and go inside the folder, there you will find the rtconfig file.

I think all you need to do is just point your colonial theme to use the images of the unzipped folder, no need to zip it back up. This is what I do with my default theme, the image resources points to Default_4.0_Unpacked, which I have modified.