Did this get resolved? I may have the same or a similar issue.
I usually have Firefox as my default browser, and run it in a Modern Mix window on the desktop.
I was trying to help out my mother-in-law over the phone, and wanted to see IE the same as she was seeing it (in Modern UI), since IE looks completely different in those two modes. But, IE was always opening in a MM window. IE didn't appear (after initial install) in the MM App Settings list, and setting Fullscreen and deselecting "Always use last state" for Modern application launch didn't affect that.
The only way I could get that to happen was to go into IE Internet Options, Programs, and deselect the "Open Internet Explorer tiles on the desktop" check box, but I could only do that by making IE my default browser.
At that point, IE did launch in Modern UI mode, and appeared in the MM App Settings list.
When I set my browser back to Firefox, it all reverted. ID has the "Open Internet Explorer tiles on the desktop" grayed out, and setting Internet Explorer to Force Fullscreen Always doesn't help. IE again always launches in a MM window.
One other odd thing. The icon next to IE in the App Settings list is the Firefox icon. Makes me wonder if MM is keeping a separate set of config info for each browser, or only has one set of info for all browsers.