Reproduction steps:
1. Open the attached “IN-113089.zip” project
2. From the Project window, select the “Model_ArmatureOnly.fbx” asset (Assets > FBX)
3. In the Inspector, open the “Animation” tab
4. Expand the “Mask” dropdown
5. In the “Definition” property dropdown, select “Create From This Model”
6. Expand the “Transform” property
7. Uncheck/disable any bone (e.g. Root)
8. Click “Apply”
9. Observe the previously disabled bone in the list

Expected result: The bone remains disabled
Actual result: The bone is re-enabled

Reproducible with: 6000.2.0a9, 6000.2.3f1, 6000.3.0b1
Not reproducible with: 6000.0.56f1, 6000.2.0a8

Reproducible on: Windows 10 (user reported), Windows 11
Not reproducible on: no other environments tested