SQL Server Database Project for multiple databases

Question

Hello,

we want to start using the SQL Server Database Projects for our databases. The thing is that we have two seperate databases with almost the same table structures, stored procedures, etc. but have a few minor differences. For example one of the two doesn't make use of a few of the tables and does have different users and permissions granted.
What would be a good way to keep the two databases on the same level?
Is it possible to keep just one database project for the two seperate databases and "deactivate" parts on one machine?

Thanks in advance! I literally appretiate all the advice given.