This is a bug I've noticed and tested a bit. What seems to be going on is that the mod isn't currently set up to recognize anything to do with the quality system.
the effect of this is that that any higher-quality items in your inventory are registered as a completely separate item and are never placed/used, where as all ghosts, regardless of quality, are seen by the mod the same way it would see a standard-quality building. What you're seeing is the standard quality items in your inventory being placed by the mod into higher-quality ghosts, in effect permanently "upgrading" that item to the quality of the ghost that was laid out.
Really hope this gets fixed at some point; at best it's completely incompatible with the Quality system and at worst it straight up breaks the game (in a cheating sense). Before I had realized what was going on in my latest game, I had noticed that I'd somehow ended up with way more Rare Assemblers than I thought I had at first but quickly put them to good use. Only later on I realized they were basically cheated, really put a damper on my run since that made a big difference to my progression. Really hope this mod gets patched soon, I've basically decided I cant use it as it exists :/
