Hey buddy,
It's kinda of manual work. One mod probably overwrites another's configuration so you'll have to manually pick each configuration you rather have.
Each <ability> node can only show up once, so you can't just append one XML to another.
Now, about having mutagens on any every skill it's a lot easier. Pick the XML you like the most and simply add the attribute maxenhancements="1".
Like this:
<ability ...>You change to:
<ability ... maxenhecements="1">Where "..." are the other attributes this ability has.
You'll have to do this for every ability in "geralt_skills.xml".
I assume you know a bit of XML and code editting. :P