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[Thiadmer Riemersma <thiadmer.riemersma@xxxxxxxxx>]

If the idea is to have a single PCB design onto which some components are
optionally placed, I use a separate application for that. I find that
preferable, because the production/assembly phase is a different phase than
the schematic/PCB design. (For example, when starting assembly, you quickly
need to also handle inventory keeping and the component ordering process.)

Managing variants of PCB desings that are largely the same, is a completely
different thing.