In case of using the Y-Sort node I think so. I've never worked with the Y-Sort node.
A solution could be to set the player node as a child of the layer (tile map) which should appear in front of the player an set the tile maps property "Y Sort" to true.
If yor problem is related only to the three things (lower layer, player, upper layer) you can try to handle this by changing the position inside your scene tree, so anything will be rendered in the correct order withou using the Y-Sort node by placing the player node between the to layers.
Anything I mentioned here is pure theoretical and could lead to other problems.
You could search on YT for "Y-Sort" and especially look for the video from Game Development Center. I remember, some time ago there has been posted a video for these kind of problem, but for isometric tilemaps. Maybe it helps though.