Yeah, in this case, it's not the "display over over apps" setting. For this one app specifically I rely on the clock (in the notification bar) to keep an eye on my time in the app. Yes, I could use other apps or my watch but sometimes my usage is spontaneous and only for a few minutes so the additional overhead is not ideal. So, I find the behavior to be a bit user hostile in hiding the clock and making it more difficult to monitor the time.
This app also has a habit of crashing or breaking my phone's wireless connectivity. I have no idea why but if I try to use the app around noon or midnight, it causes my phone to lose wireless connectivity (cellular connectivity is not affected). So, the lack of notification bar hides when that occurs (and that I'm now using metered cell service).