When calculating (checking) project permissions Permission helper (neither opened from the project page nor the one from the issue page Admin menu) doesn't consider "Granted to" items except "Project role". That says, that if the user A is in the X group and you give the ADD COMMENTS permission to this X group, there will be ability to add comments to this A user, but the Permission Helper says there is no permission because the A user does not have ... project role.

Example:
1. "Add comments" permission is added to toldot-CTO group and to Project Lead:

2. User nisbor is Project Lead and is a member of toldot-CTO group:

3. Permission helper in this project shows that threr is no ability to add comments to user nisbor: