I understand your reasoning, I just disagree that those secondary things make a pip of difference to CR. No wonder high level monsters are getting steam-rolled.
Personally I'd say a properly effective CR 13 is epic.
If most high level campaigns are saying the official high CR monsters are too weak (on a per CR basis), then you have to ask why and the proverbial fly in the ointment seems to be these secondary CR modifiers.
I'm not because I don't see the point of those secondary elements. Orcus' immunities do not affect his effective Challenge Rating IMO, they are too easily ignored.
When Orcus is likely getting dropped in one round by the majority of high level party's (I'd estimate) then something in the official CR rules smells fishy and we can trace most of that bad smell to these secondary guidelines, most of which don't actually affect Challenge Rating.
Adhering to those secondary guidelines is what's causing most of the problems in my opinion.