I'm way limited on time so I'll try to address a couple of the things.
----
Shadow Tiddlers such as StyelSheetColors are not rebuilt every time but 
they are built into a fresh empty TiddlyWiki and will rebuild themselves to 
their original state  if you delete them. AKA: If you change 
StyleSheetColors and than delete it, it will rebuild it's self to before 
you made any changes.

This is true for plugin made shadow tiddlers as well, if you change them 
they will keep your changes but if deleted and sometimes when updated they 
will revert back to their original states. 

----

>A lot of plugins create CSS "on 
> the fly" and append it to the StyleSheet tiddler. 

I'm not sure about this, I have never seen it done, and I do a ton of CSS 
editing on TWC.
Plugins Either make a shadow stylesheets or use element styling: eg <div 
class="thingone" style="border:2px #FF0 solid"></div>

As for issues with plugins that use Element level styles being cheating 
when they are not highly readable code... well I hate to say it but tough 
cookies.
Developers are allowed to make their plugins anyway they want.

That doesn't mean you can't change things if they where made right you can 
still use the !important flag in your StyleSheet to override them. eg:
<div class="thingone" style="border:2px #FF0 solid;"></div>

Can be changed in your StyleSheet tiddler by adding
.thingone {border:none!important;}

Otherwise you do like any other good hacker and learn to read machine 
optimized code.

At just so you have something visual to go off of:
<https://lh4.googleusercontent.com/-2NQEDGd51sM/UmxW7cZypoI/AAAAAAAAANA/uNuGE2Sgvxg/s1600/2013-10-26_165645.png>


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