Why does the game turn into a Metroidvania when it does? Because you're picking up from where the Soldier left off, and he is obviously the protagonist of that type of game (he even gets a Charge Beam), rather than a linear ninja platformer. You aren't playing your own game anymore, you're playing his.
The only problem here is that the Soldier's goal was the same as yours was before: Taking the scroll to the top of the mountain. Your new goal is to seek out the musical notes, which, of course, you're not going to do if you simply tread old ground. That's why it becomes a Metroidvania, because the methods you need to completely your new goal demand exploration rather than travelling to a specific location.
