### 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
float lod_distance_multiplier = p_render_data->scene_data->cam_projection.get_lod_multiplier();
	{
		for (int i = 0; i < p_render_data->render_shadow_count; i++) {
			RID li = p_render_data->render_shadows[i].light;
			RID base = light_storage->light_instance_get_base_light(li);
			if (light_storage->light_get_type(base) == RS::LIGHT_DIRECTIONAL) {
				p_render_data->directional_shadows.push_back(i);
			} else if (light_storage->light_get_type(base) == RS::LIGHT_OMNI && light_storage->light_omni_get_shadow_mode(base) == RS::LIGHT_OMNI_SHADOW_CUBE) {
				p_render_data->cube_shadows.push_back(i);
			} else {
				p_render_data->shadows.push_back(i);
			}
		}
		
		for (uint32_t i = 0; i < p_render_data->cube_shadows.size(); i++) {
			_render_shadow_pass(p_render_data->render_shadows[p_render_data->cube_shadows[i]].light, p_render_data->shadow_atlas, p_render_data->render_shadows[p_render_data->cube_shadows[i]].pass, p_render_data->render_shadows[p_render_data->cube_shadows[i]].instances, camera_plane, lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, true, true, true, p_render_data->render_info);
		}
		if (p_render_data->directional_shadows.size()) {
			
			light_storage->update_directional_shadow_atlas();
			RD::get_singleton()->draw_list_begin(light_storage->direction_shadow_get_fb(), RD::INITIAL_ACTION_DROP, RD::FINAL_ACTION_DISCARD, RD::INITIAL_ACTION_CLEAR, RD::FINAL_ACTION_CONTINUE);
			RD::get_singleton()->draw_list_end();
		}
	}
	
	bool render_shadows = p_render_data->directional_shadows.size() || p_render_data->shadows.size();
	bool render_gi = rb.is_valid() && p_use_gi;
	if (render_shadows && render_gi) {
		RENDER_TIMESTAMP("Render GI + Render Shadows (Parallel)");
	} else if (render_shadows) {