1. Should the boolean useJointCal be generalized to some calibration_method variable that could handle a variety of different methods that we might experiment with over the years, and even within active DRP?
By the time we develop those different methods, they'll be implemented as different SuperTasks with configurable output datasets, I think, and hopefully all of the driver code for validate_drp (probably renamed to something involving "verify") by then) will be too. So yes, eventually we should do this, but I think it'd be premature to do it now.
2. Can --output be made unnecessary with a Config default?
I'm afraid not; it's pretty solidly baked into pipe_tasks (which will save software versions even if you don't save any real datasets and disable config and metadata saving, as I've done). That can be turned off on the command-line by using --no-versions, I believe, but I'm not sure if even that will prevent pipe_base from creating the output directory.
3. Create a new issue to someday add a test to ci_hsc or lsst_ci.