If it’s taking 3 hours on a passenger train, a 5-10 minute transfer seems vastly more efficient.

Yes, but most people can't sleep through a train transfer

On a night train such as the Transsib that takes several days to get from A to B anyway, being able to sleep through it and not needing to lug your stuff around is usually considered more important.

(Although in some cases you are woken up for border formalities.)