It feels completely natural to me, but I think it is unintuitive, and games which feature it without explaining it are disadvantaging people with less gaming literacy.
It’s similar to the mechanic in shooting games, where reloading while there is at least one bullet in the gun results in a faster reload (because the gun doesn’t need to be cocked).
It’s realistic, but I feel that it should be ignored, in the same way each bullet from the old mag magically transfers into a new mag.