Some factory methods for `Domain' don't fully construct valid objects

[btalamini]

The Boolean set operation methods that construct instances of Domain don't fill out all the member variables. The missing ones (the mfem_*_ids_) are needed for getting indices into FiniteElementState instances.

This bug is also present in the EntireDomain and EntireBoundary methods, but I'm about to submit a simple fix for those.

[samuelpmishLLNL]

I could fix this in its own PR or roll it into the DG one (which is already making some improvements to the Domain class)-- do you have any preference?