I have tested a lot of FlyMe5 Beta Versions with the same Result.
Without Gapps WhatsApp Notification works without delay.
In the moment where i installed the Gapps the Problems beginn.
You can try the new Miui Google Installer V2.
Just unzip and install the GoogleInstaller2.0.apk.
Open the App and hit the Big Button in the Center.
The App will ask to install the Gapps One by One just press Install and Done after every App no need to hit the big red button at the end just close the App.
I have noticed it won’t work with every Beta!
For me it works perfectly on 220.127.116.11A.
After all you can update with Update App and notification will continue to work.