### 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 constexpr (p_pass_mode == PASS_MODE_COLOR || p_pass_mode == PASS_MODE_COLOR_TRANSPARENT) {
		glActiveTexture(GL_TEXTURE0 + config->max_texture_image_units - 2);
		GLuint texture_to_bind = texture_storage->get_texture(texture_storage->texture_gl_get_default(GLES3::DEFAULT_GL_TEXTURE_CUBEMAP_BLACK))->tex_id;
		if (p_render_data->environment.is_valid()) {
			Sky *sky = sky_owner.get_or_null(environment_get_sky(p_render_data->environment));
			if (sky && sky->radiance != 0) {
				texture_to_bind = sky->radiance;
				base_spec_constants |= SceneShaderGLES3::USE_RADIANCE_MAP;
			}
			glBindTexture(GL_TEXTURE_CUBE_MAP, texture_to_bind);
		}
	}
	bool should_request_redraw = false;
	for (uint32_t i = p_from_element; i < p_to_element; i++) {
		const GeometryInstanceSurface *surf = p_params->elements[i];
		GeometryInstanceGLES3 *inst = surf->owner;
		if (p_pass_mode == PASS_MODE_COLOR && !(surf->flags & GeometryInstanceSurface::FLAG_PASS_OPAQUE)) {
			continue; 
		}
		if (inst->instance_count == 0) {
			continue;
		}
		GLES3::SceneShaderData *shader;
		GLES3::SceneMaterialData *material_data;
		void *mesh_surface;
		if constexpr (p_pass_mode == PASS_MODE_SHADOW) {
			shader = surf->shader_shadow;
			material_data = surf->material_shadow;
			mesh_surface = surf->surface_shadow;