Reproduction steps:
1. Open the attached "ussvarsuib" project
2. Open UI Builder via Window -> UI Toolkit -> UI Builder
3. In the Toolbar of the Viewport, select "My Theme" as the Theme
4. Click on the "+" button and "Add Existing USS"
5. Select the "MyStyle.uss" file
6. In the StyleSheets, select "VisualElement"
7. In the Inspector, go to the Background section
8. Hover over Color and click on the three-dot menu
9. Click on "Set variable"
10. Observe the results

Expected results: Both "--red-100" and "--danger-color" show up in the USS variable list
Actual results: Only "--red-100" shows up in the USS variable list

Reproducible with: 2022.1.0a14, 2022.3.17f1, 2023.2.4f1, 2023.3.0b1
Not reproducible with: 2021.3.34f1, 2022.1.0a13

Reproducible on: Windows 11 Pro, MacOS 14.0(user's)
Not reproducible on: No other environments tested