Still unsure why the latest version is unable to login remotely to the MySQL instance with the root password when it was verified correct due to being able to log in locally.

Perhaps a clue is that the error text from MySQL came back with the username "root" (correct) appending "@local" (incorrect). So something somewhere is appending the "@" sign and the spurious domain data to the username entry. Unknown if this is normal operation for MySQL or not, or if it is something in Mantis doing it.

It is perfectly normal that the _databaseversion entry already exists in the config table - this holds the schema version, and indeed there should be only one entry. The installer will correctly execute an UPDATE statement if the record already exists.

Even though what you have done seems correct, it is not supported or recommended. You should not try to second-guess what the installer is doing to manually update the database as this may impact system operation or future upgrades.

You should rather try to figure out why your superuser DB account (root or whatever) can't connect from your webserver. Suggested reading: https://dev.mysql.com/doc/refman/5.7/en/problems-connecting.html

Thinking I didn't explain myself well.

I can use the password while remoted into the server to log in to mysql so it isn't a password problem.

I was able to use the mantis regular install process to update the database on our DEV server just fine, but on the PROD server the regular mantis install process failed.

So I checked the box to only "print the commands" used to update the database. That is where I got the commands that would be run by the installer.

Then I used those same commands while logged in locally to mysql to do the update.

The problem is that the normal mantis installer code should test if the primary key exists and if so do an Update. But it actually only does an Add. This is what I was reporting needs to be enhanced in the installer code. The error from mysql actually says that the mantis installer code is trying to do an ADD not an UPDATE.

I can use the password while remoted into the server to log in to mysql so it isn't a password problem.

By remoted into the server I assume you mean via SSH / Remote desktop session. This means that you are effectively connecting locally to your database.

Your webserver on the other hand, most likely does not connect locally, but over a TCP/IP connection. Therefore you need to authorize your privileged account (root or whatever) to also connect remotely. This may require creating a new user account root@%.hostname.com or similar; please refer to MySQL documentation for further information.

This is a MySQL setup issue, not related to MantisBT. Consequently, I will resolve this issue as "no change required".

As for the steps you used to extract the upgrade instructions, they are correct but be aware that they may not result in a fully functional database in the end, depending on the schema change (some upgrade steps execute PHP code, which cannot be translated to SQL statements).

The problem is that the normal mantis installer code should test if the primary key exists and if so do an Update

It does, but only when actually performing the update, not when generating SQL.
I'll see if this can be improved.