I think you're missing some possible scenarios from the original poll, one as you have mentioned, Rossi having influence over the decision, the other being would Movistar have influence to exert. We don't know quite how much influence Movistar have purchased, often times title sponsors are only paying a pittance toward the overall running costs.
Would Dorna influence this decision? I agree with others in that so long as Rossi is signed there, Dorna are happy that the money will continue to flow.
Have Dorna influenced the placing of riders in the past? 100% yes. Dorna were instrumental in PBM signing Yonny Hernandez at the end of 2012, they needed a vehicle to keep a rider from the South American continent in the class. Michael Laverty was only offered the other seat when Shane Byrne refused it. Despite finishing 4th in CRT and 9th in the Valencia GP, James Ellison was never even in the picture.
Dorna, while likely innocent on this occasion, do have form. They are a business above all else.
"They will let Yamaha choose". This is where the notion that Yamaha alone will choose comes into question. If you're Lin Jarvis or Yamaha MotoGP Factory Team and you're faced with the following:
1. All the top riders are out of contract at the end of 2016
2. Your primary focus is to win races & championships
What do you do? Personally, I would chase the fastest riders on the market, the men most likely to win me those races. Wouldn't you?
Ok then, so when will the details of the offer from Yamaha to Marc Marquez emerge?
It won't, because it didn't happen. Are Yamaha entirely calling the shots within that team, or is Valentino 'assisting' them? I would love to have been a fly on the wall when Mr. Jarvis reported back to Japan that they had just lost the services of the reigning World Champion.
No tinfoil hat necessary.