hello everyone. I am fairly new to Godot and game development so please be patient with my questions <3

I just started developing a single-player 2D game. The project I recently joined already has a bunch of artwork which has been created especially for this game. It's not pixel art like most 2D examples I see around in Godot. I have tons of .png files for the backgrounds and the objects of this world. I would say it's a mix between the typical Pokemon-style game experience and a fancier artsy project, but it basically looks like this

Based on my research so far, I decided to keep an image file for the background (no interaction with this layer is envisaged atm) which I included as TextRect, and I am trying to build layers of rocks, plants and other interactable objects on top of that. I typically have 1 object per image file, from which I draw the tiles without particular problems. But when I try to Y-sort the rocks to move around them (I have already created a Collisions Layer in the Physics Layer menu) I find myself manually defining a collision shape for each tile of which my rock is made...
Here is my basic node tree:

and a capture of my TileSet editor:

How can I ask Godot to consider my rock as 1 object, with a unique Y-sort origin and collision shape, spreading across different tiles ?
I tried following this tutorial but when he clicks on the tree and easily creates a collision shape in the tileset editor, I cannot do the same. My editor looks like the picture I posted above.

Also: does it make any difference, in relation to this rock issue, if I get rid of the TextRect and automatically generate a background of little identical grey tiles, which would then become my main TileMap node ?

my world scene currently looks like this:

I understand that I'm not using tiles as they are meant to be, so I am looking for a way to integrate all the pre-existing artwork into the project.
many thanks in advance for the help ^^
I've been wrapping my head around these questions for a few weeks now...