I recently learned that editing metrics in Wikistats actually exclude edits to deleted pages, for consistency with the old Wikistats.
For many years now, researchers have generally agreed that it is preferable to include these edits in editing metrics, to avoid the confusion that occurs when page deletions cause historical metrics to change long after the fact (this is called "deletion drift").
For this reason, all the metrics produced by Product Analytics (including the key product metrics and wiki comparison tool) include these edits. This adds another layer of confusion; for example, I spent a couple of hours investigating T293660 before realizing that the differing treatment of deleted edits had caused the discrepancy.
To help minimize this confusion, Wikistats should have the option to switch between with-deleted and without-deleted versions of editing metrics. I strongly recommend that with-deleted be the default, but if there's disagreement about that, at least providing the option would be very helpful.