PSA Performance Issues?

I am currently experiencing some performance issues and think it might be related to the clustered indexes in PSA & maybe staging. 

Could you please let us know if this has been raised before and whether there’s a setting in regards to the type of index used?

BimlFlex has options to control table creation and indexing. You can override the indexing through the PostCreateSql extension point by injecting a post create update.
        
There is no specific setting that controls the indexing of the staging/persistent staging tables. 
        
You can also use the SSDT project to override the entities generated by BimlFlex, as well as define deployment post processing that can update the target databases when needed.

There are also several performance options for the SSIS processing, as well as the staging and persistent staging SQL processing that might affect load performance.