Little bit of oops there hwhalen...
The midi editor theming is part of the theme but is indeed not WALTER (think of WALTER as optional advanced scripting for certain parts of a theme),
most of it can be edited in the theme editor, which is
not a function of the preferences dialog. Actions window, sir.
Notice I said it
can be edited in the theme editor, but it doesn't have to be : that's just a convenience for editing a .ReaperTheme file, which is a text file and can be edited in any text editor. Which is the kind of thing you might like to do if you wanted, for example, to copy a load of midi editor colours from one theme to another...
First place to start would be the
2. Common tweaks to a REAPER theme sticky, to learn how to unpack a theme. Then open the .ReaperTheme file in a text editor and look for midistuff.