Database Design for Managing Main and Custom Scope Entities

I have a database consisting of a main scopes table (containing standard scopes), a projects table, and a configuration table linking scopes to projects. I now need to allow for custom scopes that are unique to each project. These custom scopes shouldn't be stored in the main scopes table so that users don't see scopes from other projects when configuring their own. However, creating a separate table for custom scopes causes issues with referencing two different tables using foreign keys. What are some best practices or design patterns to handle this situation?