There are a bunch of scenarios where there are standby passengers on a flight who need seat assignments -- overbooking the flight is just one possible cause.
If you miss your connection are you willing to pay for a seat on a different flight since in your scenario the airline held your seat on the original flight and didn't assign it to a standby passenger? Because what happens right now on major US airlines is they put you on standby on the next available flight if they can't guarantee you a seat or get you a confirmed seat if possible at no additional charge.