Avinash ag0759
I received a very good and detailed feedback from the support team (Thank You Support!). It helped me understand the legacy (history), sequence of architected solution and the solution architecture itself. I agree with Support's detailing and inference.
Here's a simple reverse engineering, Two Authentication Schemes (unique to each UserStore i.e. one Custom AuthScheme for DB2 and other for AD). This means Two Authentication URLs, which means Two Federation Objects (Legacy or Partnership). Two Legacy Federation Objects means, Two SharePoint Connections, thus two powershells scripts i.e. two TIPs. Hence even if we make the IdentifierClaim the same, underlying they are two different TIPs. Thus what has been architectured currently is correct.
As I mentioned if we want to move away i.e. Getting you to a single TIP, with Single IdentifierClaim, will need to revamp the entire solution. This will impact not only the SharePoint WebSites, but also beyond that e.g. unifying into a single authentication scheme, which means you'd need to cascade the custom authentication functions to another component.
Alternatively you could check with Microsoft Support for inputs as recommended in the case.