How i like that idea very much. I do not thing it will be the case.
On a active route in the navigation. Zoom in on a waypoint. You'll see kind of two routelines overlapping eachother.
What this tells me. A route is a chain of mulitple miniroutes. Where every waypoint is both start and endoint. As long as the deviation stays with in the same miniroute. MRA is flexibel doesn't do strange things overall. But when the deviation causes to interact with two (or more) of these miniroutes (skipping waypoints). Things starting to be complicated. To start a new (mini)route, you need to end the previous one first.
It looks like this the basic structure how the Here platform works.