The Redgate comparison technology works on objects within a database.  If you are using linked servers, here's some reference material that may help. 

Discovering three or four part names in SQL Server database code

Database Build Blockers: Cross-Server Database Dependencies
Note: This material references SQL Change Automation, which is Redgate's SQL Server only migrations solution.  Flyway is our x-database, x-OS migrations solution so the concept is similar.