It seems like logged actions from Wikidata that are marked as bot are treated as non-bot actions when I see my watchlist on English Wikipedia. It appears that the problem happens with logged actions only, not edits.
With [Latest revision][Page creations][Logged actions][Wikidata edits][Human (not bot)] turned on, my watchlist has this line (which is not an expected behavior):
(diff | hist) . . Dm Early modern human (Q15978631); 17:55:07 . . MsynABot (talk | contribs) (Protected "Q15978631": Highly used item: to be indefinitely semi-protected per Wikidata:Page protection policy#Highly used items; please use Template:Edit request on the item talk page if you cannot edit this item ([Edit=Allow only autoconfirmed users] (indefinite)))
For comparison, with [Latest revision][Page creations][Logged actions][Wikidata edits][Bot] turned on, my watchlist has this line (which *is* an expected behavior):
(diff | hist) . . Dmb Versailles, Yvelines (Q621); 10:55:35 . . AVMbot (talk | contribs) (Changed claim: Property:P1082: 85,862, Add France 2018 population; Changed an entity: Add France 2018 population)
Ideally, both should be shown only when [Bot] is turned on as a watchlist filter.
On my Wikidata watchlist, both are treated as a bot edit/action.
Link to the edit I gave as an example above:
Link to the logged action I gave as an example above: