Reproduction steps:
1. Open the attached project "ReproProj"
2. Open UI Builder (Window > UI Toolkit > UI Builder)
3. Click Project in the Library window of UI Builder
4. Add the element: "Custom Controls/MyElements/MyElement" into the Hierarchy
5. Save the UXML file
6. Open the UXML file in a text editor
7. Observe

Expected result: "MyElement" tag is “<elements:MyElement />” and custom xmlns are present
Actual result: There is no custom xmlns set, and the "MyElement" tag is “<MyElements.Runtime.MyElement />”

Reproducible with: 6000.0.58f1, 6000.2.8f1, 6000.3.0b5, 6000.4.0a2

Testing environment: Windows 10 Enterprise 21H2
Not reproducible on: No other environment tested

Notes:
- Reproduction was done by following the steps in this documentation: https://docs.unity3d.com/6000.2/Documentation/Manual/UIE-define-a-namespace-prefix.html