When shift-clicking items to put them in a slot, they transfer but they are still displayed in the player's inventory and they are not displayed in the machine's slot. On the contrary, when shift-clicking to take off items from a TR inventory, they are still displayed in the inventory but not in the player's inventory. The displaying updates when going out of the GUI.

yeah, I noticed this. I will take a look at some point.

It also updates when trying to pickup the ghost items!

👍 to this, I might look at the code myself. It even seems to behave different on client/server as an item will sometimes end up somewhere else once I close the GUI.