### 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
atlas_rect.size.width = shadow_size;
		atlas_rect.size.height = shadow_size;
		zfar = light_storage->light_get_param(base, RS::LIGHT_PARAM_RANGE);
		if (light_storage->light_get_type(base) == RS::LIGHT_OMNI) {
			bool wrap = (shadow + 1) % subdivision == 0;
			dual_paraboloid_offset = wrap ? Vector2i(1 - subdivision, 1) : Vector2i(1, 0);
			if (light_storage->light_omni_get_shadow_mode(base) == RS::LIGHT_OMNI_SHADOW_CUBE) {
				render_texture = light_storage->get_cubemap(shadow_size / 2);
				render_fb = light_storage->get_cubemap_fb(shadow_size / 2, p_pass);
				light_projection = light_storage->light_instance_get_shadow_camera(p_light, p_pass);
				light_transform = light_storage->light_instance_get_shadow_transform(p_light, p_pass);
				render_cubemap = true;
				finalize_cubemap = p_pass == 5;
				atlas_fb = light_storage->shadow_atlas_get_fb(p_shadow_atlas);
				atlas_size = shadow_atlas_size;
				if (p_pass == 0) {
					_render_shadow_begin();
				}
			} else {
				atlas_rect.position.x += 1;
				atlas_rect.position.y += 1;
				atlas_rect.size.x -= 2;
				atlas_rect.size.y -= 2;
				atlas_rect.position += p_pass * atlas_rect.size * dual_paraboloid_offset;
				light_projection = light_storage->light_instance_get_shadow_camera(p_light, 0);
				light_transform = light_storage->light_instance_get_shadow_transform(p_light, 0);
				using_dual_paraboloid = true;
				using_dual_paraboloid_flip = p_pass == 1;
				render_fb = light_storage->shadow_atlas_get_fb(p_shadow_atlas);
				flip_y = true;