I have had the tvOS 11 beta profile installed on my X since 11.1.1, and have not received a system update notification since then (still currently on 11.1.1).
Prior to my X, I had the tvOS 10 beta profile on my 7 Plus with iOS 10.1.1 and it blocked update notifications, too. However, tvOS 10 beta profile does not seem to block update notifications when I had it on my X. Only tvOS 11 beta profile - probably has something to do with iOS version of your phone.