I experienced the following problem:
If I disable the notification scheme for a project, I will be notified if someone mention me in a comment field.
Do you have the same bug?
@mentions are separate. As long as a user has view access to an issue, if they are @mentioned they will be notified as the message is set to direct to them. It's not a bug but there are other posts on this matter.
Depending on the add-ons you have you maybe able to disable them
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