When searching with the Maniphest Advanced Search, using a parent project tag works as expected, returning all tasks tagged with the parent project or with any subproject (or sub-subproject, etc.).
However, when trying to use the "Not In:" feature with the parent project tag, the search will only exclude tasks tagged with exactly the parent project, still returning all tasks from all subprojects.
Run this for a baseline search.
Run this to see the Diffusion v3 subproject tag excluding the original task from the search as expected.
Run this to see how exclusion does not work with parent project tag.
Using parent project tag in search to exclude tasks excludes all tasks in itself, and also all subprojects/milestones.
Only tasks tagged with the exact project name are excluded.
Tested on the Phacility instance a couple of minutes ago, it reproduced here successfully with above steps.