This would have happened on Server 2012 R2 as well, dual scan has been around and causes a lot of problems as you noted.
It is strange that I didn't have these issues in 2012 R2. I essentially copied the same GPO for 2012 R2 and made some minor changes to it to convert it for 2016. My 2012 R2 show the correct default service.
Weird, I have various Server 2016and now 2019 with WSUS and while dual scan was an issue for me on Server 2012/ 2012 R2 not anymore.