I can't imagine MVDS is happy about getting Honda strong-armed into taking Miller. They pooled a lot of resources into getting that ride and partnership with Estrella Galcia to create their own Moto3-GP pipeline, I can't see them taking kindly to getting Miller forced upon them.
Maybe Honda will run MVDS two bikes next season, maybe even full factory packages. Seems to me LCR is over holding Miller as a financial liability with all their funding problems this year. I just can't imagine Miller taking a factory ride away from Rabat at MVDS and their owner being chill about it. Billionaires tend to get what they want.
With Aspar's financial problems maybe HRC sees MVDS as a more stable team and is giving a second bike to Miller there, that is the only way I see this going down. I think its very likely Aspar will be out of GP by 2017 unless they partner with a factory and become a defacto satellite 2 team like Pramac or Tech 3.
With the 2017 rule changes everyone is going to look to partner up once the manufacturers are forced to supply extra rides at a fixed price. Up to 4 additional bikes per factory, with costs mostly covered by Dorna.
2016 is a financial survival season. 2017 is where the real rides and money come in from Dorna. If a team can hold onto their spot until 2017, they will be permanent fixers on the grid with their choice of bikes. That is everyone's endgame and focus right now, it would be so shitty to lose your spot in 2016 when 2017 has "free" money and "free" bikes of your choosing.
Edit: Everyone should do a quick read of the bullet points for 2017. Its going to be a big year.
http://www.crash.net/motogp/news/217806/1/ezpeleta-outlines-2017-motogp-proposals.html
Edit2: Interview with Ezpeleta on MotoGP.com that goes more into detail
http://www.motogp.com/en/news/2015/04/18/new-motogp-manufacturers-agreement-in-the-works/174071