Hi,
Actually I am not sure.
Messages or rather iMessages sent to you are effectively sent individually to each device.
"Sync" in this case only means "Display on All devices".
Over the life of iMessages people have "complained" that removing an iMessage on one device does not remove it on another.
Related to that is of course the Notifications.
For myself I have the iPhone set to "Send from" the iPhone Number and the Mac set to the Apple ID.
This made it easier to test sending to the iPhone from my Mac in the early days (since El Capitan entering your Own Name does not bring up your Contact Address Card details - you have to manually enter the iPhone number to "call it").
Which ID the iMessages is addressed to makes a difference as to which device will receive it "first" - which in turn does have some effect on the feedback of "Delivered" and "Read" at the senders end (the last depend on whether you are sending Receipts)
Ergo depending which ID the iMessages are effectively sent to can then have an effect on the Notifications.
On the Mac if Messages is the "Front" app you tend not to get Notifications. (it is one way they have already reduced the Notifications when you have several devices in close proximity).
I think you have suddenly noticed what has been a gradual change.

9:04 pm Thursday; September 22, 2016
iMac 2.5Ghz i5 2011 (El Capitan)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
iPhone and an iPad (2)