Just to clarify, AppScale uses Cassandra as the database backend for the datastore API. In the AppScalefile, that is what the "database" role indicates (which machines should run Cassandra for the datastore API).
AppScale does not currently have support for managing a MySQL server. You can still connect to one with your AppScale app, but you'll need to start and manage the MySQL server yourself. It sounds like you've already done this.
Since AppScale does not manage the MySQL server, you do not need to include it in the ips_layout of your AppScalefile in order to make it accessible to your app. Depending on how your network is set up, you may need to expose the ports of your MySQL service. I don't have much experience with Docker, but https://docs.docker.com/v17.09/engine/userguide/networking/
might be helpful. Is the port that MySQL is running on accessible to the container that AppScale is running on?