[Plugin: Theme Tweaker] how exactly does this work?

Theme Tweaker inserts text css blocks in the pages that your server dishes out. e.g.

<!-- Theme Tweaker (start) -->
<style type="text/css">
body {background-color:#E8E1C4;color:#1D1B29;}
...
</style>
<!-- Theme Tweaker (end) -->

It does not overwrite your style.css, which indeed it cannot, unless you have your file protection bits as 777.

Theme Tweaker only reads your main style.css file pointed to by:

$stylefile = get_theme_root() . '/' . $mThemeName . '/style.css' ;

It doesn’t try to follow the @Import directives, so it may not work well for WP-MU.

I don’t have WP-MU and haven’t done any test on it. The only feedback I got from one user is that it did not work for him for a particular theme, although he says it worked for other themes.

my file permissions are 775, and owned by apache user, but I can change this…
But is the plugin made to overwrite the style.css if the right file permissions are set?
so you think there shouldn’t be anything unsafe here?

Yes, the plugin is safe. It never tries to write anything on your server. And, if/when you deactivate it, everything reverts back to your original styles/colors.

btw. there was a very similar plugin years ago, except for the ajax effects, but it would also show the names of the elements where those colors were applied and it also would allow (if I remember right) to change background images.

Have a look here, I think this is the last mod: https://pastebin.com/pastebin.php?dl=f4ce9cdb9

if you could incorporate all those features into your plugin, I think all wpmu users woudl be extremely grateful ??