I think I was able to figure it out. Go to Settings -> Notifications -> Advanced Settings -> Floating notifications -> and select Bubbles. Hope this helps!
That worked, only that Facebook Messenger bubbles still don't work exactly as they used to. At least now the bubbles appear. But the experience isn't the same.
I have a solution that worked for me.update messenger to latest version if it's not already.uninstall it. Download messenger version 240.0.0.12.120 from APKmirror. Install that version,login in your account,enable chat heads in the app,then go update the app from play store. Hope it helps.