When I put attributes on the body such as

body {
 background-color: grey;
}

It does not even show in the developer console that I even tried to add this attribute. Normally if it did not work because of an override I would at least see it crossed out.

Only happens in the new designer.

I like to use pure CSS backgrounds which look good, load fast, and do not save to the repository. I am just giving a simpler example in this post which can obviously be done in the theme designer.