I don't think you can apply the "complete runs" rule to a "flex" 90.

What I see most on rooftops is absent from all these pics....the flex coming loose, or being broken. Whether this is because of folks tripping over it, or just general weathering, I don't know.

I do try to run my stuff in a manner that conforms more closely to the contours of the roof, and the equipment.
To avois punching holes in the roof, I attach my stuff to wood "sleepers" (short pieces of 2 x 4) that are in turn attached to the roof with roofing cement.