Rather than incompatible parts simply not appearing when ships are loaded, it would be nice if there was a special part that fills the spots. It could also bring up a tooltip, like in the tutorial, which would explain that there are parts which are incompatible with your current version or mods.
#Incompatible parts indicator
shut sedge
umbral meadow
Maybe a special structure tile?
shut sedge
That could work!
umbral meadow
The problem now that I think about it is that if a part is missing then its size is unknown.
shut sedge
Would it be possible to include the ship's footprint in the metadata? That way the game could fill in any of the unexpected gaps with the special structure
umbral meadow
It would be possible yes, but wouldn't be retroactive for existing ships/saves.