Used them for at least the last 6 years and love them.
Like BrunsNick said they make a small notch on the center line so that the mold picks that up, it is on the back side of the thumb so you don't feel it. When the insert is made from the mold that leaves that small mark on the insert and that mark is lined up on the center line of the new ball.
As long as the new thumb hole is drilled at the same pitch then the inserted thumb insert will be oriented and pitched the same way.
The mold will pick up every little nuance of the thumb hole, bevel, taper, etc.
If you leave tape in the hole it will pick that up as well including the texture of the tape.
Just be sure to use a thumb hole in a condition (size) that you can use when your thumb is at it's maximum size. You can still add tape when your thumb shrinks.