If you want to change the visible parts of a given model, you should use different MTL files changing the transparency factor in [font=courier new]d[/font] lines ([font=courier new]d 0[/font] being fully transparent and [font=courier new]d 1[/font] fully opaque). As the MTL file used by an OBJ file must be cited in its [font=courier new]mtllib[/font] line, you won't have any other choice that creating different OBJ files.
But it's not a problem to have different pieces citing the same value in their [font=courier new]model...#[/font] property and a different value in their [font=courier new]planIcon...#[/font] or [font=courier new]doorOrWindowSash....#[/font] properties. There was a bug in the Furniture Library Editor some time ago about this but it was fixed in version 1.20.

By the way, here's a version 1.22 of the editor with IDs if needed. I promise the choice of the columns editable in the editor will end up in preferences one day [edit: removed link, IDs can now be displayed with an option in preferences]