So, for anyone following this, I have made it work for my project, but, I used the shadows only for the scenario, that means only for the tilemap, any player or object is going to have another type of shadow, not generated by the LightOccluder, much like oldschool pre-rendered shadows.
So, what I did is split up the light occlusion into 2 layers:
Layer 1 -> Walls (The occlusion poly should encapsulate the outer part of the wall)
Layer 2 -> Floors (The occlusion poly should only mark the bottom of the wall)
If I want the a lamp behind a wall, I simply uncheck the wall layer, the light only affects the floor tiles now. But the catch is, for every light in the game, I need two lights, one that will affect the walls and the other the floor. There's still some limitations, but I am getting nice results so far,
But that does not solve all the problems, some overlapped shadows break the depth illusion, I just need to be careful with the light placement position.
-My hopes are that in the future, Godot will have a feature more easy to implement for handling shadows with YSort, or something like it.