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As per title, PopupButton.isTransparencyModeEnabled only works if the control is enabled. Once disabled, the borders etc render again.
If anyone else runs into the problem, a (bad) workaround till fixed is to override the Control Template, and in the trigger for isEnabled, add something like:
<Setter Property="BackgroundDisabled" TargetName="contentArea" Value="Transparent"/>
<Setter Property="BorderBrushDisabled" TargetName="contentArea" Value="Transparent"/>
<Setter Property="BackgroundDisabled" TargetName="PART_IndicatorArea" Value="Transparent"/>
<Setter Property="BorderBrushDisabled" TargetName="PART_IndicatorArea" Value="Transparent"/>