correct Nick
if Timecerts have been fitted then the studs will remain loose when they are at the correct height, that doesn't matter, since when the nut is fitted on top of the head and tightened pressure is put onto both ends of the threaded stud, this might even be better than stock because the threads at both ends are doing the work, with a stud "bottomed" in a crankcase stud the pressure is applied to the wrong side of the thread formations, and of course when it gets tightened the laws of physics determine that the pressure will then transfer to the other side of the thread formation, but did it? has it? etc etc, much better (well slightly) for it to happen all by itself and the stud stretch along its length, with both stud threads equally sharing the torque.
I now routinely Timecert all 12 crankcase studs whenever I see them, lets face it they have been working as stock for maybe 40+ years, you have to refresh everything from time to time.
CLEM