Now, I wouldn't necessarily think that the Elemental Punches won't be available through Move Tutors because they were so widely available from Emerald to the most current Platinum. The reason why is because not everyone has purchased these games, and to make full use of the tutors, the Elemental Punches may more than likely be brought back in as Move tutor attacks. You are correct on why they cannot be held as TMs though and that is because of cross compatability with DPPt. However, I wouldn't be surprised seeing the Elemental Punches available through Move Tutors at all.
In time Flying types will eventually be given better attacks that are powerful and deals no damage to the user. At the start of RSE theu begun this thought with Aerial Ace and Sky Attack. Then, in DPPt they made available a strong Brave Bird. Now, I wouldn't expect anything new in these remakes, but more than likely in a Fifth Generation game we will be given an even better Flying type move for battle.
Now, if the legendary beasts were awarded their own signature move that DPPt may have coding for, then I definitely think your idea can work. Actually, more than likely it could happen in which their movepools are updated a bit from what DPPt has given them. However, I would only see an entirely new move for these three if DPPt can recognize it.