Commentaire officiel
You can use our "Georeferenced w/Manual GCPs" workflow (the one on the right). It allows you to do exactly what you are describing for associating pixels with coordinate locations.
We intend to add a linear mission planner in a future release of Map Pilot to enable pipeline, power line, river and road surveys.
Currently people are doing all the linear sections using Map Pilot and then joining the individual segments into one map using our the Location Map feature in Maps Made Easy.