Please allow IT Administrators to disable the popup messages for anything. If this application is going to truly be the replacement for Skype For Business (as I've heard), treat it like a business application. I tried going in to my messages and was greeted by a popup notice that I should download the app on my phone. I closed it and went to go select a user, and poof it popped up again immediately.
This is just a nuisance of a feature that should not be in a messaging platform designed for business use. If I want the app on my phone, I'd get it, stop shoving it in my face while I try to use the app.