For starters....perhaps the original threaded hole was NOT tapped with a "bottoming" tap.
There are 3 basic types of taps....starters (almost look like they start with a point)....taper tap (less point but not yet square all the way to the end)...and bottoming tap (full thread to the very end of the tap).
You can see where using a bottoming tap in any hole will create threads all the way to the bottom of the drilled hole.
For studs, I suspect the makers want the stud to tighten up before hitting the very bottom of the hole.
If you make threads all the way to the bottom, how do you know when the stud is tight in the thread or just hitting the bottom without locking into the threads?
Bob

Good explanation about the tap-sets being #1 Starter, #2 middle and #3 bottom tap to make threads right to the bottom.

To maintain the 135 mm measurement from case to the top of the stud, I found that sometimes the stud doesn't bottom out. Loctite will stay pretty solid and really hold the stud.

BTW: When the stud is tightened against the bottom to get the 135 mm, it'll lock the threads by pushing the stud upwards.

It's very important to re-check the torque on the studs after about 1000 Miles. You'll find that some studs need a little more tightening to get the 23-24 ft-lbs torque.