Comments as below:
2> Did not get you! what do you mean by " but it creates multiple xsds based on target namespace, it needs to be manually merged and then compared."
3>The best practice is how you import the XSD while creating the IS document. You can generate single document or you can generate sub structures docs.
Let me know how are you generating it. Kindly share the screen shots.
#webMethods#Integration-Server-and-ESB