On a recent trip out west (and my first encounter with big mountains), I flight planned and filed my route using the same waypoints that define the airways I wanted to follow, in order to cross the Sandia mountains into Albuquerque at the published airway minimum altitude of 10,000 ft. My route was OTTO VOR to CYOTE Intersection (near the crest of the Sandia's) to ABQ VOR to KAEG Airport. When nearing OTTO, the controller gave me an amendment to my route. She said "After OTTO, cleared to KAEG via Victor 60 to ABQ VOR." So I looked at the chart on the iFly for a minute, scratched my head, and keyed the mike.
"CENTER, Mooney 76 November with a question..."
"Go ahead."
"I don't see where my route amendment changes my flight path at all. Am I missing something?"
"No Sir, it doesn't change your route at all. But by putting you on airways instead of waypoints, I can keep you at 10,000. Otherwise, I'd have to climb you to 12,000 since the MORA in that area is 10,400."
So I learned that unless I specifically file airways, my minimum safe altitude is ruled by the MORA even if my waypoints define an airway. I guess when flying between waypoints you aren't bound by the same lateral limits like you are on airways. I must have missed that nugget of info in ground school and thought I'd share it.