I agree that this configuration is inelegant, but I'm not immediately sure how we could do better without significant work.
I'm reluctant to add anything explicit to the configuration of the task that generated the catalog, since this isn't configuration for that task but for the transformation.
Nicer would be to manipulate the schema. Ideally it would be possible to add some sort of indication to individual fields that they should be copied, but I don't think afw::table supports that sort of annotation (other than by overloading the doc strings). I may have missed something though, so I'll dig into that a bit further.
A third option might be to add a static method to the measurement task itself which returns a list of fields to copy (in much the same way as we do for the measurement plugins at the moment). Again, this feels quite invasive on the source tasks, but maybe it's the best option.
Suggestions welcome; I'll give this some more thought when I have time.