Just a guess - but it may be that the line-up only happens when the marked tooth on one gear sits exactly between the two marked teeth on the other. This happens with the markings on a Douglas T35 for example.
The T35 cams have 48 teeth, driven from a 24tooth gear on the crank via an idler (36Teeth). So far, so good.
Then - the idler between the 48T magneto gear and the 24T crank happens to have 39 teeth - an odd number.
When the punch mark on the crank gear crest tooth lines up, it meets a punch mark on the idler tooth valley.
Still so far so good.
Now the fun. The magneto gear goes on where only the "other" side of the idler can be seen. Magneto gear also has a punch mark. The back of the idler has two. One for TDC. and one to match up to the magneto gear mark for spark timing. That last one cannot be exactly on a tooth. They settle for two marks, on two consecutive teeth, intending that the magneto mark tooth goes "in the gap" as the gears mesh.
I do not say that is also the situation with the CW, but it might something similar.