Why does adding a transactional replication publication change all the tables and columns to "not for replication"?
Not sure if you have checked this; but there is an option in sp_addarticle called @identityrangemanagementoption. If set to manual, then it "Marks the identity column using NOT FOR REPLICATION". Pls check if this is the case.

Ref : https://msdn.microsoft.com/en-us/library/ms173857(v=sql.110).aspx