Yeah, I'm looking for something exactly like this.
I've tried just adding things to replace registry values in the same manner the My Computer, My Network Places, My Documents and Recycle Bin does, but it doesn't accept them. The syntax is just the same in the .theme file though.
I think what has to be done is whatever reads the ".theme" files has to be altered to accept more changeable registry values.
In theory the themes could not only change more icons in the theme, but could also replace the LogonUI.exe's value with another one. Changing logon screens for different themes.
Does anyone know what program/app/file reads the .theme files? I'm a novice programmer, and I might be able to alter the necessary thing to accept more values if I knew...