There are such strange bevahiors with notifications right now:
Muting a server is explicitly said to be turning off notifications and unread messages sign UNLESS you're mentioned. At this moment notifications are not produced at all, even if you're mentioned, you'll just get a red circle with digit next to the channel and server you were mentioned in, no sound, no notification, but weirdly enough you can have push notifications sent.
Muting a channel has the same behavior, it ignores notification settings completely. Say, if you set the channel to produce notification for every message, muting this channel will turn notifications off, same will happen if you set notifications for mentions only in a muted channel.
While the first case seems pointless to even allow the second one has a sense to it, i would like to be able to turn off unread messages sign from a channel but to be notified when i'm mentioned (moderating a server but having channels that you are not interested to read).
Also you can't make exceptions for some channels if there is a server-wide mute. Ability to do so could be useful for the same case to be notified.
Everyone and here mentions now don't produce even digits if setting to ignore them is on but this is probably a desired and long time requested behavior.
All in all this should be more flexible, notifications should be configurable independently of unread message sign.