Game devs are just not that familiar with beds. They rarely have the luxury to use one, most often sleeping at their desks.
My favorite stalker bug is the two dudes in the second kind of hub area that just constantly repeat their lines.
“Get out of here, Stalker! Get out of here, Stalker! Get out of here, Stalker…”
“What are you waiting for? I said come in, don’t just stand there! What are you waiting for? I said come in, don’t just stand there! What are you waiting for? I said come in, don’t just stand there!”
In programming, everything is just an object in a space. If the devs decided that the object cannot clip and needs some sort of margin, this happens. It’s a decision of design and if the same design philosophy is kept, you’ll always see this.
In some games, you might see a short animation of someone getting into a bed, during which you can’t move. After that, the objects bed and player will be fused, as if they form one object. Maybe the game is better suited for meeting them separate, who knows. Considering the large number of different objects, you might be surprised how it is possible players aren’t clipping through everything.
If it’s to avoid clipping, then something is badly wrong in the older game, where the person walks inside a bunk bed, lies down, then sinks all the way through the bed before rising up to slightly levitate above it!
Although in that case the idea of a margin might make sense, since at the end they’re only barely above the bed. In the new game they’re in the right place at first, and then rise up like a foot and a half above the bed once the player approaches them…