It's just my assumption but it's possible Soken might have just been too busy with final sound and music coding for Stormblood - apparently coding a certain music file to play on a certain mount is not a simple task (as shown by how long it took to change the magitek armour's BGM to Terra's Theme).

Also I don't really feel Pa-Pya is really appropriate as a mount theme, it's a little too light and breezy for a mount, even if said mount is a giant flying egg...