For example, if team="company" has "READ", and team="company/dev" has "WRITE", and Bob is in team="company/dev" but not team="company", then Bob will have both "READ" and "WRITE" because of his membership in team="company/dev"; the API will give no indication that the "READ" indirectly came from team="company".
Also, the permissions that the PAT needs in order for GraphQL to even list those things is excessive.
Anyway, here's my audit script for such things: https://github.com/datawire/collaborators
I have added two output examples. One for when you only want to find users that have been directly assigned to a repo (DIRECT) and one that shows how their roles and team memberships decide what permissions they have on a repo.
Yes, but if it's just being implied then it won't list "READ" separately in the "permissionSources", it will just list "WRITE".