It appears that “My Colors” exist at the Workspace Level, it may be the same for “My Gradients” (although they may exist at the Site Level). The question” Is there a way to manage (Create, Delete, Edit) these things at the level they exist? Right now they are tucked far away in the “Section>Design>Background>Color” area. They should be first class citizens and managed at the Workspace or Site area, or possibly in the Library. Is there a way to manage “My things”?
Have you got any screenshots of the “My colors”? As far as I’m aware, all colors and at the site level. Both Wix Studio and the Wix Editor have support for some form of “global” color system that are available within color pickers.
There will be occasions where you can add colors outside of those global styles - depending on the specific needs of your site.
If you’re working in Studio, this article will give you more insights into working with colors - Studio Editor: Working with Site Colors | Help Center | Wix.com