I think it's all about the riders' pace, and reseeding, although it may seem to have been done unfairly several times up to now, is still a necessary evil due to safety reasons.
Surely it depends on how knowledgable those doing the reseeding are (how well they know the pace of the riders they reseed) - and how objectively and fairly they place the reseeded rider
For me the most danger lies when riders of vastly different levels of skill are thrown on the course together. One is fast, the other not so much, add in dust and things get dangerous fast.
Example: say Chaleco has a mechanical and finishes almost last (like Jonah and his electrical gremlins in '11). this is a guy that is Dakar podium material / potential. Do you reseed him in 130th the next day? That is just asking for trouble. He will be pushing through too many riders that are much slower than him, which is a liability to both parties. It is impossible to control how reckless drivers of his calibre will be to make up positions, and how many chances they will be willing to take. It is what they do for a living and what puts food on their table (with all due respect to the privateers)
I still think reseeding riders last at the end of their respective "speed group" (easily determined looking at times / average speeds) is still the safest option for rallies.