I got MM the day it was released and have played through it more times than I can count, and I have never seen a second cutscene at that tree. The only cutscenes I can think of that show Skull Kid and the fairies are at the beginning, at that tree, and at the end of the third day (on clock tower).

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Caress the one, the never fading rain in your heart- the tears of snow-white sorrow.
Caress the one, the hiding amaranth in a land of the daybreak.