### 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
shader_data_request_func[RS::SHADER_FOG] = nullptr;
	material_data_request_func[RS::SHADER_SPATIAL] = _create_scene_material_func;
	material_data_request_func[RS::SHADER_CANVAS_ITEM] = _create_canvas_material_func;
	material_data_request_func[RS::SHADER_PARTICLES] = _create_particles_material_func;
	material_data_request_func[RS::SHADER_SKY] = _create_sky_material_func;
	material_data_request_func[RS::SHADER_FOG] = nullptr;
	static_assert(sizeof(GlobalShaderUniforms::Value) == 16);
	global_shader_uniforms.buffer_size = MAX(4096, (int)GLOBAL_GET("rendering/limits/global_shader_variables/buffer_size"));
	if (global_shader_uniforms.buffer_size > uint32_t(Config::get_singleton()->max_uniform_buffer_size)) {
		global_shader_uniforms.buffer_size = uint32_t(Config::get_singleton()->max_uniform_buffer_size);
		WARN_PRINT("Project setting: rendering/limits/global_shader_variables/buffer_size exceeds maximum uniform buffer size of: " + itos(Config::get_singleton()->max_uniform_buffer_size));
	}
	global_shader_uniforms.buffer_values = memnew_arr(GlobalShaderUniforms::Value, global_shader_uniforms.buffer_size);
	memset(global_shader_uniforms.buffer_values, 0, sizeof(GlobalShaderUniforms::Value) * global_shader_uniforms.buffer_size);
	global_shader_uniforms.buffer_usage = memnew_arr(GlobalShaderUniforms::ValueUsage, global_shader_uniforms.buffer_size);
	global_shader_uniforms.buffer_dirty_regions = memnew_arr(bool, global_shader_uniforms.buffer_size / GlobalShaderUniforms::BUFFER_DIRTY_REGION_SIZE);
	memset(global_shader_uniforms.buffer_dirty_regions, 0, sizeof(bool) * global_shader_uniforms.buffer_size / GlobalShaderUniforms::BUFFER_DIRTY_REGION_SIZE);
	glGenBuffers(1, &global_shader_uniforms.buffer);
	glBindBuffer(GL_UNIFORM_BUFFER, global_shader_uniforms.buffer);
	glBufferData(GL_UNIFORM_BUFFER, sizeof(GlobalShaderUniforms::Value) * global_shader_uniforms.buffer_size, nullptr, GL_DYNAMIC_DRAW);
	glBindBuffer(GL_UNIFORM_BUFFER, 0);
	{
		
		ShaderCompiler::DefaultIdentifierActions actions;
		actions.renames["VERTEX"] = "vertex";
		actions.renames["LIGHT_VERTEX"] = "light_vertex";
		actions.renames["SHADOW_VERTEX"] = "shadow_vertex";
		actions.renames["UV"] = "uv";
		actions.renames["POINT_SIZE"] = "gl_PointSize";
		actions.renames["MODEL_MATRIX"] = "model_matrix";