Krzysztof Findeisen, I think I've got this fixed - I reproduced the original problem, and was able to inspect the repo after conversion with this fix to see that the deepCoadd dataset was defined properly.
All changes are in obs_base - I was able to find a way to make this the default behavior while still letting HSC override; see code comments.
The last commit there is the only directly relevant one - the second one is just adding the logging I used to diagnose the problem, and the first is just minor cleanups I made en route to that.
PR is https://github.com/lsst/obs_base/pull/249
Jenkins is green: https://ci.lsst.codes/blue/organizations/jenkins/stack-os-matrix/detail/stack-os-matrix/31936/pipeline/