This seems like odd behaviour to me. Basically I have a query set up that has a filter " Not In: Games Project". When I view that when logged in, it gives me back a list of tasks that are not in Games Project. However "Games Project" is not visible to public users, and when the query is run for them (either on the dashboard or through Maniphest), no results are returned.
This is the query: https://code.redpointgames.com.au/maniphest/query/0JCVlyLIg0F_/
And this is a task that I would expect to appear in the search results (it appears in the search results only when I am logged in): https://code.redpointgames.com.au/T2287