Nice idea to open a dedicated topic, we started to talk here:
KiCad: The case for Database driven design - #202 by craftyjon
about that but i think a dedicated topic is more appropriate.
Right or wrong i don’t know, like many other things it must be decided on the use case.
This is how i do it up to now:
- in the component database i have, there is a field ‘do not place’ that i fill in when i place parts on the schematic.
- the field is extracted in the BOM i send to the manufacturer, the P&P file contains the position of the part.
so the manufacturer is in charge of modifying the P&P file that i send him, i’m not particularly happy about that, there is a ‘grey area’ of responsibility in the process… things can go wrong (and indeed has gone wrong several times 
)