Could this prevent the shortcut from being processed correctly?
I don't think so. In early Alpha versions, Microsoft used a different application ID for the CD and the MS Store version, but this has been abandoned for the release ( at least this is what Asobo told me, I never seen the CD version ), so they both share the same app id so, from the installer point of view, they are exactly the same. If the sim wasn't recognized, the installer wouldn't even proceed.
Just to be sure, do you have this file ?
%LOCALAPPDATA%\Packages\Microsoft.FlightSimulator_8wekyb3d8bbwe\LocalCache\Content.OPT
If yes, go to the last line, and tell me where the InstalledPackagesPath line points to:
InstalledPackagesPath "xxxxxxx"