### 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
inst->flags_cache = flags;
		GeometryInstanceSurface *surf = inst->surface_caches;
		while (surf) {
			
			if (p_render_data->screen_mesh_lod_threshold > 0.0 && mesh_storage->mesh_surface_has_lod(surf->surface)) {
				
				Vector3 lod_support_min = inst->transformed_aabb.get_support(p_render_data->cam_transform.basis.get_column(Vector3::AXIS_Z));
				Vector3 lod_support_max = inst->transformed_aabb.get_support(-p_render_data->cam_transform.basis.get_column(Vector3::AXIS_Z));
				
				float distance_min = (float)p_render_data->cam_transform.origin.distance_to(lod_support_min);
				float distance_max = (float)p_render_data->cam_transform.origin.distance_to(lod_support_max);
				float distance = 0.0;
				if (distance_min * distance_max < 0.0) {
					
					distance = 0.0;
				} else if (distance_min >= 0.0) {
					distance = distance_min;
				} else if (distance_max <= 0.0) {
					distance = -distance_max;
				}
				if (p_render_data->cam_orthogonal) {
					distance = 1.0;
				}
				uint32_t indices = 0;
				surf->lod_index = mesh_storage->mesh_surface_get_lod(surf->surface, inst->lod_model_scale * inst->lod_bias, distance * p_render_data->lod_distance_multiplier, p_render_data->screen_mesh_lod_threshold, indices);
				/*
				if (p_render_data->render_info) {
					indices = _indices_to_primitives(surf->primitive, indices);
					if (p_render_list == RENDER_LIST_OPAQUE) { //opaque
						p_render_data->render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_VISIBLE][RS::VIEWPORT_RENDER_INFO_PRIMITIVES_IN_FRAME] += indices;