Maybe it is time to make some separation between “Plot for Printing Documentation” and “Gerber Creation for Sending to Fab”?
“Do not tent vias” is clearly a Gerber Fabrication specification.
“Exclude PCB edge layer from other layers” is also a Gerber Fabrication specification.
“Plot sheet reference on all layers” could mean either to someone like me who has never clicked the box and examined the outcome.
AFAIK at the moment, “Exclude pads from silkscreen” is a “Plot for Printing Documentation” feature.
Might I suggest:
Gerber File Specifications
I’ll bet a quarter this question gets asked again after V5 release.