Reproduction steps:
1. Open the attached “IN-109761.zip” project
2. From the Project Window, open the “MyDocument.uxml” in UI Builder
3. From the Hierarchy, select “MyCustomControl”
4. In the Inspector under Attributes, expand the My Test > My Class > My Reference properties
5. Modify the “My String” or “My Int” field values and observe them

Expected result: All modified fields should show as overridden with "dirty" marking in the UI Builder Inspector
Actual result: SerializeReference fields (“My String” and “My Int”) are not marked as dirty

Reproducible with: 6000.2.0b1 (1618a92a88ac), 6000.2.0b12, 6000.3.0a3
Not reproducible with: 6000.0.54f1, 6000.1.13f1, 6000.2.0a10

Reproducible on: macOS 15.5 (M4 Max), Windows 11
Not reproducible on: No other environment tested

Notes:
- Only the “My String” property (which is a direct reference) under “My Class” foldout behaves correctly and shows the override
- If the fields are shown as dirty at the very start, left-click on any of the properties and select “Unset all” and then perform the reproduction steps