I’m sorry, I’m not quite understanding your question.
If you’re talking about the RIGID definitions in the rmsd evaluation, then those regions are what *you* want them to be. Rosetta doesn’t have any requirements that those match to any sort of secondary structural regions. In the Meiler lab tutorials, those regions are specified against the transmembrane region of the protein because that’s what the person who put the tutorial was interested in. For their example protocol, the exact positioning of the loops was less important to their scientific question than what was happening to the transmembrane helicies. But that’s entirely a scientific decision, rather than a techincal one. You should base the RIGID definitions based on the regions of the protein that are of scientific interest to you. If that includes some loops, then include the loops. If you’re not (scientifically) interested in the very ends of the alpha helix, then omit those residues, and only include the middle part of the helix.
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