If you want to get technical this works due to how the engine handles entities and more importantly how saves handle entities.
All entities are stored in a list, and the order of this list is the key to if you can use something to clip into the ground or not.
When you trigger a level change all the entities in the new map get loaded into the list first. After that any entities from the previous map’s entity list that transferred over (ie where within the trigger_transition) get loaded in the same order they where previously stored (this includes the player)
When you make a save the list is stored in the same order, and when you load a save it loads the entities in the same order.
When the player entity is loaded it checks to see if it’s stuck and if it is it clips downwards. Now say a metrocop tossed up a manhack at some point as you’re playing and you try to use it for clipping; this manhack is now stored at the end of the list, or more importantly, it’s stored after the player entity.
Since the entities are loaded in the same order the player would load first and check if it’s stuck, which it is not at this point in the loading process, and after that the manhack will spawn, so the clip failed.
Now if you leave the manhack (outside the transition trigger) and enter a new map and then go back the engine will start by loading all the entities in that map into the list, which now includes the manhack, and after that it loads the player so now the manhack is before the player in the entity list and thus will be loaded first when you load a save so now when the player is loaded it will check if it’s stuck and it will see that it is because the manhack has been loaded this time around and so you clip into the ground.
I hope this makes somewhat sense to someone