mediawiki.special.watchlist/watchlist.js should use a timestamp parameter in the api call to mark all pages as seen, so that changes that haven't loaded yet are not missed.
As a user,
When I load my watchlist,
And click "Mark all changes as seen",
Only changes that were made prior to loading the watchlist should be marked as seen,
So that any changes made between loading and clicking "mark all changes as seen" are not missed