[Possibly spoiling both the glyph trunk puzzle & the tree arcade puzzle.]
My amateur understanding of the tree arcade puzzle is that the arrow points from the starting point to the ending point (e.g. from white to red). However, you have to rotate the arrow (and thus, both the starting & ending point) when a circle makes an appearance. Based on the earlier puzzle (the treasure chest), a circle above = 90 degree counterclockwise, a circle below = 90 degree clockwise. So the circles cancel each other out when both appear.
Hope this helps! I'm stuck at a later part fwiw, haha