Clustered Primary Key

For background, we're using Campaign Classic V7 with a fully on-premise architecture. In the documentation for data model 'best practices' it states this:

For SQLServer database, you could consider using “clustered index” if performance is needed. Since Adobe does not handle this, you need to create it in SQL.

I added a clustered primary key via SQL to the NmsRecipient table and performance improved as expected. Great. The problem, however, is when I run the "Update database structure...", it always wants to drop the index because it's not defined anywhere in the XML I guess. 

Is there anyway to avoid that? I'd imagine if the documentation says to create in SQL then there has to be some way of atleast making the system accept\ignore whatever you deployed directly via SQL. Anyone have any idea how to do that???