RE: Management Reporter in GP 2016
Dave -
Not sure I am understanding your precise situation. You write "They are all in the same database, just different instances." I read "they are all on the Same SQL Server, but using different SQL instances (i.e. SQLServer1\Company1, SQLServer1\Company2, etc.). This sounds like you're using different Dynamics (System) databases on various instances of SQL for different companies. Please let me know if I am wrong.
If I am right, you would encounter difficulty trying to configure more than one connection to multiple GP/SQL instances - you'll get an error that says "The integration you're trying to create already exists." When trying to connect to subsequent Dynamics databases to provision companies in Management Reporter, once the first one is configured. In my experience you cannot configure multiple GP connections through one MR installation.
If this is simply a matter of having multiple companies in the same Dynamics (System) database, then it works just fine.
All that being said, our team, and I am sure a number of other partners, have done many unification projects to bring disparate system databases together to support consolidated reporting and improve multi-company processing.