On some further thought, I think it is, in general, better that most scoring sorts of code takes a set of particles describing the (for example) protein, at the desired level of detail instead of a Hierachy from which they extract such a description. This allows the user to select the resolution used without having to maintain different hierarchies with leaves at different resolutions.
More concretely things like the em::FitRestraint which takes a set of particles are doing the right thing. It allows the user to have a fully atomic model of a protein, instead to pass the residues to em::FitRestraint when it is a low resolution map. (That said, it should probably take XYZRs instead of particles :-)
Likewise, the rmsd(XYZs, XYZs) function is much nicer than the reject rmsd(Hierarchy, Hierarchy) since you can choose to compute rmsd on a residue or domain level.