You cannot earn AAdvantage or WorldPerks Q-miles on RootsAir, just on Alaska's program which means you are starting from scratch with a FF program unless you're from the west and have had a membership in their program. You can cash in for awards on AA and NW, but you are not putting these miles into your current accounts with those carriers.
What these fares suggest is that the market has really softened and RootsAir cannot fill its planes, even at their previously advertised prices. The fares given are equivilent to AC's upgradeable V-fare, which only gets you into Silver. The Gold fare is $100 more each direction. It means RootsAir is teasing us by giving us the upgrade without using certificates. Is the RootsAir ticket fully flexible, or are you locked in? What is the advance purchase requirement? If you are locked in, the MHD may still be more flexible. Of course, hardly matters with only a couple of flights a day.