I am currently struggling with the same problem: An application which is made of several "base" components which all could have their own database objects.
I tried the option to put all in the same schema and using different flyway meta tables, but this does not work: When flyway comes to process e.g. the second table for the second module and discovers that the schema is not empty (because the first module has migrated its db changes), it stops, as flyway has now no chance to determine the state of the db and its migrations.
Also using base line versions do not help, as in that case the changes of the base line would be skiped for the next modules... I think the only reasonable solution with flyway would be to use different schemas....