It turns out this discrepancy exists because Wikistats excludes edits to deleted pages from its calculation for consistency with the old Wikistats, as @kzimmerman noted. I hadn't realized that this was the case; including deleted pages is the preferred way to construct metrics these days, to prevent numbers from shifting long after the fact.

My investigation is in this notebook.

The main thing that would prevent confusion like this is having the option to see both with-deleted and without-deleted versions of editing metrics in Wikistats. Just having the option will increase awareness of the importance of that parameter and give users the capability to quickly determine when it's the source of a discrepancy like this. I've filed T295212 for that.

Reopening while I make some documentation updates to wiki comparison and possibly our data dictionary as well.

I've added notes about this to the "metric definitions" tab of the Wiki Comparison Tool and to mw:Wikimedia Product/Data glossary.