Thank you for post into the forum.
I am little confused with the contents of your post.
If you are refering to the full qualification of objects name inside the Stored Procedure Code or Function or View, I suspect the answer will be no.
SQL Compare will not rewrite the code for you. The purpose of SQL Compare is to generate a set of results that show you the differences between objects in each data source and provide a mechanism for deployment or synchronization to make the objects in each data source identical.
If this is a feature that you wish to be added, I recommend that you post on the Red Gate Uservoice Forum using this LINK.