Sorry but you are not making any sense.
1- With the cache off, if you put a rule like #wrapper {background-color:red;} in Advanced Options > Head Section > Custom CSS Rule box. does it work?
If not, can you leave that specific rule in so we ca have a look.
2- What do you mean by “I am seeing this….”
The message you mention is inside the style sheet and meant to make sure people DO NOT edit the style sheet directly as you should never edit theme files.
So are you trying to edit the style sheet? Where / how are you seing the message?
What do you want to stop exactly. Weaver automatically generates its style sheet based on the options and the custom CSS that you place in the Admin pages, this is the way it works, so I do not understand what you are trying to stop.
Please focus on what you are trying to accomplish, what you are doing to do that, and what is not working. See next for what we were testing before