### 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 (material->uniform_set_updated) {
			material->uniform_set_updated = false;
			sky->reflection_dirty = true;
		}
		if (!p_transform.origin.is_equal_approx(sky->prev_position) && shader_data->uses_position) {
			sky->prev_position = p_transform.origin;
			sky->reflection_dirty = true;
		}
		glBindBufferBase(GL_UNIFORM_BUFFER, SKY_DIRECTIONAL_LIGHT_UNIFORM_LOCATION, sky_globals.directional_light_buffer);
		if (shader_data->uses_light) {
			sky_globals.directional_light_count = 0;
			for (int i = 0; i < (int)p_lights.size(); i++) {
				GLES3::LightInstance *li = GLES3::LightStorage::get_singleton()->get_light_instance(p_lights[i]);
				if (!li) {
					continue;
				}
				RID base = li->light;
				ERR_CONTINUE(base.is_null());
				RS::LightType type = light_storage->light_get_type(base);
				if (type == RS::LIGHT_DIRECTIONAL && light_storage->light_directional_get_sky_mode(base) != RS::LIGHT_DIRECTIONAL_SKY_MODE_LIGHT_ONLY) {
					DirectionalLightData &sky_light_data = sky_globals.directional_lights[sky_globals.directional_light_count];
					Transform3D light_transform = li->transform;
					Vector3 world_direction = light_transform.basis.xform(Vector3(0, 0, 1)).normalized();
					sky_light_data.direction[0] = world_direction.x;
					sky_light_data.direction[1] = world_direction.y;
					sky_light_data.direction[2] = world_direction.z;
					float sign = light_storage->light_is_negative(base) ? -1 : 1;
					sky_light_data.energy = sign * light_storage->light_get_param(base, RS::LIGHT_PARAM_ENERGY);
					if (is_using_physical_light_units()) {