The MP215 is a fixed calibration and can't be modified. It uses a Cobb AP, but it is locked to the tune and you can't swap tunes at a whim, you get the MP215 tune and that's it, plus once it's on the cat's ECU you can't go back to stock without going to the dealer and having them reset things. With the Mountune branded Cobb AP you get a normal Cobb AP, but in addition to the Cobb OTS tunes you also get a tune that is done by Mountune with 45 days of support for tweaks based on your data logs.
The Mountune AP costs the same as the Cobb AP and comes with all the same OTS maps, plus a 'custom' Mountune map that they will revise for you so it is the better buy if you're going to go with an normal, standalone AP rather than buying from Cobb where you don't get retune work from Randy. The MP215 is very static and it is what it is, no changes unless you buy the upgrade to the MR230 kit and you can't use the AP it includes for other people's OTS stuff, nor can you reflash back to stock or such things. The benefit is that it still gives pretty solid performance and you get to keep your warranty intact as long as you follow the rules and have it all installed by a Ford dealer, or Mountune themselves if you're lucky enough to live close to their US shop.
TL;DR - Go with Mountune's AP over Cobbs because of tune support plus you don't lose anything because you can still use Cobb's OTS stuff and other OTS tunes. Go with the MP215 if you don't have a desire to constantly change and tweak things and you want to keep your warranty.