The Flyway Database migrations (see
DS-2167) currently to not work for XML-based Configurable workflow. As XMLWorkflow requires modifications to the database itself, these migrations need to be run via Flyway, instead of being run manually (as Flyway discourages changing the database manually in any fashion).
I've got a PR fix on the way. Will also require some minor updates to the XMLWorkflow documentation to detail how to enable it in 5.0.