Attached screenshot is the Dynamic Notifications app, not the stock active display.
Sent from my Moto X
Ok, here is your answer:
Open Dynamic Notification, click advanced options. Now click advanced options in the drop down menu.
UNCHECK "Use Immersive mode"
The status bar will probably show, but problem solved. Its immersive mode that causes the message to appear.
Any app that uses immersive mode will trigger the pop-up.
I don't think its the apps issue...more like a 'bug' in android. Not sure if I would even call it a bug...there just isn't any option anywhere to turn off the immersive mode "swipe down" messages. I imagine it was intentional....cause you just know that 10,000 people would call in to tech support saying they're stuck in full screen and can't get out.
I guess this is one advantage active display has over dynamic notification....that and power saving. AD doesn't actually wake your phone...one of the co-processors in the "X8" system is able to provide the notifications while sipping battery power.