Sounds like the sensitivity for supervision of that device may have been improved. Yes, it would be expected, depending on how long it loses power, for an offline malfunction to occur if you cut power to the overhead.
Looking at the history these notifications are generated by the System Actions to Watch notification rule. You could eliminate malfunction notifications from that rule, but it would cover all device.
Also now that I get two messages, one for the Liftmaster Gateway and one for Garage Door, wondering if I have it set up correctly. I have these two as Automation Devices, the LiftMaster showing as Gateway and the Garage Door as Garage Door.
That’s normal, the Gateway is the portion connected to the internet, the overhead or universal hub, and the door itself is separated because the door and gateway can have status malfunctions independently. In this case your MyQ devices stop communicating all at once and malfunction occurs.