I have a SQL Server database with the default schema and a custom schema. So for example two tables might be database.dbo.table1 and database.customschema.table2.
I want to keep the "customschema" under source control, and I have loaded that into my Visual Studio SQL Server Database Project.
When I use the Tools -> SQL Server -> New Schema Comparison... utility, it returns differences for all database schemas.
It would show all the "dbo" tables as being different/deleted in the database project even though I don't intend to keep them in the project under source control.
Is there a way to limit the results to show differences between my database project and the actual database for the "customschema" objects?
I would say no. The documentation for using Schema Compare explains the options for filtering, which can only exclude types of objects:
ApexSQL also notes this on their page about database comparison (emphasis mine):
I think if you want to filter out a certain schema you will need to use a different tool. We use Redgate tools (SQL Change Automation, SQL Source Control) and they allow you to define a filter file to exclude certain objects.