### 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
} else if (p_render_list == RENDER_LIST_SECONDARY) { 
						p_render_data->render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_SHADOW][RS::VIEWPORT_RENDER_INFO_PRIMITIVES_IN_FRAME] += indices;
					}
				}
			} else {
				surf->lod_index = 0;
				if (p_render_data->render_info) {
					uint32_t to_draw = mesh_storage->mesh_surface_get_vertices_drawn_count(surf->surface);
					to_draw = _indices_to_primitives(surf->primitive, to_draw);
					to_draw *= inst->instance_count;
					if (p_render_list == RENDER_LIST_OPAQUE) { 
						p_render_data->render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_VISIBLE][RS::VIEWPORT_RENDER_INFO_PRIMITIVES_IN_FRAME] += mesh_storage->mesh_surface_get_vertices_drawn_count(surf->surface);
					} else if (p_render_list == RENDER_LIST_SECONDARY) { 
						p_render_data->render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_SHADOW][RS::VIEWPORT_RENDER_INFO_PRIMITIVES_IN_FRAME] += mesh_storage->mesh_surface_get_vertices_drawn_count(surf->surface);
					}
				}
			}
			
			if (p_pass_mode == PASS_MODE_COLOR || p_pass_mode == PASS_MODE_COLOR_TRANSPARENT) {
#ifdef DEBUG_ENABLED
				bool force_alpha = unlikely(get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_OVERDRAW);
#else
				bool force_alpha = false;
#endif
				if (!force_alpha && (surf->flags & GeometryInstanceSurfaceDataCache::FLAG_PASS_OPAQUE)) {
					rl->add_element(surf);
				}
				if (force_alpha || (surf->flags & GeometryInstanceSurfaceDataCache::FLAG_PASS_ALPHA)) {
					render_list[RENDER_LIST_ALPHA].add_element(surf);
				}