The pane (SC 789) and two different booklet stamps (SC 789a and SC 797a) in my collection are all exactly the same size.
I'm not aware of any other uses of this issue.
The booklet stamp is four-sided perforated 13.0 x 13.3.
The two booklet stamps have the same 12.0 x 12.5 perforations.
Copying and reversing the larger stamp's top margin on top of the smaller stamp's top margin, the horizontal perforations are a perfect fit.
Moving the larger stamp closer to the smaller stamp shows a very small discrepancy in the vertical perforations.
This suggests that the size difference is not due to stretching or shrinking the stamp by soaking.

Unless anyone else has an explanation why the larger version exists, I suggest that you submit it for certification.