Correct, depending on rate of decent/climb, you may pass through the desired altitude by a few hundred feet and then return to it.
In a decent the easy solution is just to "transition" early and set the QHN prior to the 2000 limitation. So set QNH when cleared to an altitude below TL yet still prior to the 2000' limitation gives the autopilot plenty of time to catch the large down drop in altitude from changing from STD/29.92/1013 to QNH.