ya same here like im in my friends tardis and he disappears then i leave the tardis and hes gone and sometimes he leaves and i dont know

they do not turn invisible, they simply get teleported to the extirior inside the box itself (Not in the interior) but i like this idea seems more realistic

It happens mainly because there's (to my knowledge) no way of freezing the player while being able to intercept their movement controls. E.g. freeze the player at the console while still giving them the ability to look around and fly the tardis in third person, so I have to essentially despawn the player and put them in spectate mode.