### 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
return MaterialStorage::get_singleton()->shaders.scene_shader.version_get_native_source_code(version);
}
SceneShaderData::SceneShaderData() {
	valid = false;
	uses_screen_texture = false;
}
SceneShaderData::~SceneShaderData() {
	if (version.is_valid()) {
		MaterialStorage::get_singleton()->shaders.scene_shader.version_free(version);
	}
}
GLES3::ShaderData *GLES3::_create_scene_shader_func() {
	SceneShaderData *shader_data = memnew(SceneShaderData);
	return shader_data;
}
void SceneMaterialData::set_render_priority(int p_priority) {
	priority = p_priority - RS::MATERIAL_RENDER_PRIORITY_MIN; 
}
void SceneMaterialData::set_next_pass(RID p_pass) {
	next_pass = p_pass;
}
void SceneMaterialData::update_parameters(const HashMap<StringName, Variant> &p_parameters, bool p_uniform_dirty, bool p_textures_dirty) {
	update_parameters_internal(p_parameters, p_uniform_dirty, p_textures_dirty, shader_data->uniforms, shader_data->ubo_offsets.ptr(), shader_data->texture_uniforms, shader_data->default_texture_params, shader_data->ubo_size);
}
SceneMaterialData::~SceneMaterialData() {