As far as I can tell (not being a MediaWiki coder), the 'comma' method of article counting is a complete fiction, and has been so for many years now. I believe it may be time to give up on this feature entirely, and remove the option from the software (or, alternatively, implement the feature in a way that actually does what is advertised).
It appears that on wikis that use the 'comma' method (among Wikimedia wikis, currently only enwikibooks and ptwikibooks: T29256), instead of a non-redirect in a content-namespace being counted as an article if it contains a comma, such pages are counted as articles if they are merely nonempty. (If I am wrong about this, someone please say so!)
Presumably because some Wikibooks were counted differently, they were not included in the monthly article recounting that has been happening since 2015 (T68867). Now those wikis have been recounted, along with all other Wikimedia wikis (T187845), and that "complete" recounting is about to become a regular occurrence (T59788).
For this reason, I suggest that the enwikibooks and ptwikibooks communities be notified that 'comma' based counting is not actually working the way they think, ask them to choose 'link' or 'any' as a replacement method, remove mentions of the 'comma' method as a viable option in our documentation (e.g., the mw: page linked to in the first sentence above), and remove all traces of it from the MediaWiki code.