I would need to check to be certain but I believe, in my experimentation with sending notifications to slack, that messages sent via API (which is what we’re doing, under the hood) don’t cause the @channel and @here aliases to work the same way that a user typing in the UI would. This was discovered when I was messing around with a chat bot but that’s been my experience.
Outside of that, customizing the Slack notifications is not something we currently support but we can get you a vote for that feature idea. @RyanVeitch do you know of a topic for that off the top of your head?