Muscle energy is not containdicated in those patients you have listed. HVLA is.
Muscle energy is also most commonly done "away from the barrier" --> thus it is indirect.
And the source I am using is myself. When I have spent time shadowing or doing early clinicals, I most commonly see ME & CS.
The most common somatic dysfunction we have seen is either a muscle restriction or a tender point. Although HVLA is commonly used as well, it has those contraindications that you mentioned, and as you know there is a high percentage of elderly in the patient population.
(On a side note, let's assume soft tissue is always done prior to these other techniques---especially HVLA.)