My theory:
Pale Tree is a manifestation of the Dream, Mordremoth is a manifestation of the Nightmare. The two could be linked, and Mordremoth only lives in Nighmare form. However, just as all sylvari are born from the dream, what if Scarlet was born from the nightmare? What if she, unlike the Nightmare Court which merely pays service to the Nightmare, is actually an avatar of the Nightmare? Just as the Pale Tree has its own avatar, it could be that the Nightmare does as well.
In simplest terms, what if nightmare and dream coexist on the same plane, and the nightmare (read, mordremoth) has decided to use the pale tree as a means of escape? Nightmare Court set the stage, and Scarlet is the herald. Mordremoth herself could be soon to follow.
Imagine if the ancient races who originally fought the Dragons used the seed of the pale tree to contain Mordremoth? Think about it, it serves dual purposes because the sylvari are a built-in safety mechanisim. If Mordremoth were ever released, or any of the dragons were to awaken, the dream, the pale tree, and the sylvari would also emerge to fight them. As Zhaitain's corruption did not affect the Sylvari, this already paints them as a weapon created by the ancient races to combat the dragons. They're the ace in the hole, the secret gambit the ancient races placed in the hands of future generations to help turn the tide.
Of course, this is one of those things where the fact that I said it means it won't actually happen.