### Godot version

v4.0.beta.custom_build [96f12040c]

### System information

Windows 11/64, RTX 3070, Vulkan

### Issue description

From beta10 to the current master, depth prepass is broken. 

Alpha
![image](https://user-images.githubusercontent.com/632766/210395481-1eb4a6be-da4e-423f-a169-65a4b08b9411.png)

Depth Prepass
![image](https://user-images.githubusercontent.com/632766/210395511-7bb2058c-0784-46de-a582-c4d911fc8d88.png)

Alpha
![image](https://user-images.githubusercontent.com/632766/210395568-d168d393-6681-488f-b7d7-b1d58e7728ed.png)

Depth Prepass `depth_prepass_alpha`
![image](https://user-images.githubusercontent.com/632766/210395630-c9a11673-52c1-45c2-890d-29d4330f1cda.png)


Depth Prepass Beta 10
![image](https://user-images.githubusercontent.com/632766/210395836-e1c2be64-378c-4bb0-ac81-a3e9b7e7685a.png)


Note that the shadows render fine, as does vertex animation.

I also get a lot of vulkan errors that I don't get in b10. Many repeats of these on load, but not continuous:

```
ERROR: Condition "!named_textures.has(key)" is true. Returning: RID()
   at: get_texture_slice (servers/rendering/renderer_rd/storage_rd/render_scene_buffers_rd.cpp:357)
ERROR: Texture (binding: 0, index 0) is not a valid texture.
   at: (drivers/vulkan/rendering_device_vulkan.cpp:5465)
ERROR: Condition "rid.is_null()" is true. Returning: rid
   at: _allocate_from_uniforms (./servers/rendering/renderer_rd/uniform_set_cache_rd.h:129)
ERROR: Condition "!uniform_set" is true.
   at: compute_list_bind_uniform_set (drivers/vulkan/rendering_device_vulkan.cpp:7807)
ERROR: Uniforms were never supplied for set (0) at the time of drawing, which are required by the pipeline
   at: (drivers/vulkan/rendering_device_vulkan.cpp:8006)
ERROR: Condition "!rt" is true. Returning: RID()
   at: render_target_get_override_depth_slice (servers/rendering/renderer_rd/storage_rd/texture_storage.cpp:2688)

```

I'm bisecting now....

### Steps to reproduce

See MRP. Change alpha on the tree.

### Minimal reproduction project

You can use my demo from #63675
https://github.com/godotengine/godot/files/10256553/test_zorder.zip
}
		if (scene_state.cull_mode != cull_mode) {
			if (cull_mode == GLES3::SceneShaderData::CULL_DISABLED) {
				glDisable(GL_CULL_FACE);
			} else {
				if (scene_state.cull_mode == GLES3::SceneShaderData::CULL_DISABLED) {
					
					glEnable(GL_CULL_FACE);
				}
				glCullFace(cull_mode == GLES3::SceneShaderData::CULL_FRONT ? GL_FRONT : GL_BACK);
			}
			scene_state.cull_mode = cull_mode;
		}
		RS::PrimitiveType primitive = surf->primitive;
		static const GLenum prim[5] = { GL_POINTS, GL_LINES, GL_LINE_STRIP, GL_TRIANGLES, GL_TRIANGLE_STRIP };
		GLenum primitive_gl = prim[int(primitive)];
		GLuint vertex_array_gl = 0;
		GLuint index_array_gl = 0;
		
		if (surf->owner->mesh_instance.is_valid()) {
			mesh_storage->mesh_instance_surface_get_vertex_arrays_and_format(surf->owner->mesh_instance, surf->surface_index, shader->vertex_input_mask, vertex_array_gl);
		} else {
			mesh_storage->mesh_surface_get_vertex_arrays_and_format(mesh_surface, shader->vertex_input_mask, vertex_array_gl);
		}
		index_array_gl = mesh_storage->mesh_surface_get_index_buffer(mesh_surface, surf->lod_index);
		if (prev_vertex_array_gl != vertex_array_gl) {
			if (vertex_array_gl != 0) {
				glBindVertexArray(vertex_array_gl);
			}
			prev_vertex_array_gl = vertex_array_gl;