Well, if this is by design, I have to say that it's a really bad design decision. To give you a real world example, as of right now our Avast licence is about to expire and I haven't had time to calculate the number of clients/servers in order to buy a new license. So the consequence is that, for example, Powerpoint presentations are interrupted by this reminder. If this happens at the wrong time, it could be a major problem.
I thought that this was a bug, and I could have lived with it for now - since the license expires rather seldom and I would assume that it would be fixed next time it happend. But if this is indeed a design decision, i e that you have a feature that let's you, for whatever reason, disable pop-up's, and then have another feature that ignores that setting, then it's really saying to your paying customers that you know better than us whether we actually wants to show pop-up's or not. I would strongly advice you to have another discussion regarding this design decision.