The answer is...
This was definitely related to the the dc name case issue. First issue is is that the Microsoft article https://learn.microsoft.com/en-us/troubleshoot/windows-server/identity/optimize-dc-location-global-catalog is missing some srv records that the mnemonics remove. That means that the best way to verify is to use the C:\Windows\System32\config\netlogon.dns file. Copy it before applying the settings, then after they are applied, verify that the netlogon.dns file has been modified. After that check if the srv records defined in the old netlogon.dns file are actually removed. I made a script verify those entries and also let me know if there are duplicates. https://github.com/Misha305/PoshScripts/blob/main/DCNetlogonDNSChecker.ps1
In my case I still have a handful of 2012r servers and 2016 server (this one created the duplicates I suspect). I also have a 3rd party ipaddress management system. When I tried to delete the duplicate srv records with a powershell command against the 2012 r2 servers they were immediately there again. When I tried to delete them against the 2016 server they would go away for a couple of minutes, but then be re-added again. DNS server logs showed that the Ipam server was re-adding them again. Interstingly enough, while DNS saw the duplicates the ipam server did not.
To actually delete the records, I had to delete them from ipam, query the 2016 server until one of the duplicate records had been removed via replication. Once it was removed I removed the remaining via pwershell against the 2016 server and queried all the dns servers in my environment the changes had replicated and the records were all gone. I used another script to query dns to make this a little easier. https://github.com/Misha305/PoshScripts/blob/main/DCPublishedDNSCheck.ps1