If you change "Synchronize Position" and/or "Allow Ownership Transfer on Collision" checkbox and save scene, that change are not be saved. If you open another scene and open previous scene, you'll see that modification are lost.
Tested with: VRCSDK3-UDON-2020.04.09.16.59_Public
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Details:
I checked UdonBehaviourEditor.cs. EditorGUI.BeginChangeCheck() is miss placed. It should be placed before first EditorGUILayout.Toggle(...)