Layout - production "variant" - removing some footprints without affecting copper

As I said, look into assembly drawing scripts and work with them..

Just to make my point for the concept here is a view of the component table in EEschema in a KiCAD nightly from 13th May this year (the stables don’t have this, but you can have those fields as well and work with them in a stable):

If your assembly drawing script is able to get those fields from the schematic and omit the ones that are not assembled you get what you want.
I really thought the path forward would be clear after @Andy_P s answer.. otherwise I would have elaborated and added all this in my earlier post.

Your custom script ‘just needs’ to:

  • identify how many options exist
  • create drawings based on number of options

You need to be vigilant about ID convention for options, so the script knows what is together.
And you need to tell it what the basic ‘omnipresent’ parts are.. ‘_’ as ID field works for me.

PS: You can either run your own local atomic parts library or even do it with the KiCAD libs.
You just have to ADD this field in the EESchema options here BEFORE you start with the schematic or nowadays you can add them afterwards with KiField:

Any part placed in your schematic will have this field then - won’t work for already placed parts. You need to use KiField for that and ADD the field there.

PPS:

I don’t think you’ll see something like this appear for a long time.
Your best shot is doing it yourself based on the work by others.. naturally depending on your python scripting fu.