Footprint shape "silk" property or rule.
All shapes in a footprint should have a default property or rule called "silk" which can be enabled or disabled. When enabled the shape will show up on the PCB layout and in the silk Gerbers.
This would allow the ref to show up in the schematic view, but be hidden in the PCB view and Gerber.
There should be another property called Keepout, which has the shape show up only in the PCB view and not in the Gerber.
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