While we're discussing this, I'd like to know how people declare this in Altium. I know Altium has ECO tags you can use, and it also has variants, but both seem... off.
back in the SDT/PCB386+ days I just prefixed a component's value with '*' (e.g. *10k) and made an appropriate note in the drawing/assembly files. I can still do this, but there must be better ways.
I do two ways:
1. Set a field to DNP, typically Comment, Value, Description or MFGPN. Null or delete unused parameters (e.g., no MFG). Better not to enter a default value (that is, if you mean to specify a value---IF it were to be placed---as a default), in case the assembler takes that as instruction to place a part there instead.
2. Use Assembly Variants. This is what it's there for, of course! Use the schematic Compiled View tabs to graphically inspect, set and modify alternates, or set them from the variant dialog. Make sure the OutJob is set to use variants, and that at least the BOM uses the variant (but preferably all outputs, so you capture parts placement, and yes even 3D view, with the variant).
Nice part about variants is you can set non-component footprints to DNP, and include them on the BOM as such, so there is no question about what should go where. Often, assemblers will ask about so-and-so, like, should we place anything on FID1, FID2 etc.? -- obviously not, you might say, because those are fiducials, graphical features -- but they ask to make sure, and specifying as such in the BOM answers that question immediately.

Heh... well... the better assemblers ask, I suppose a cheaper one might just go ahead and assume what you meant. All the more reason to be as specific as possible.

Tim