### 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
uint32_t shadow_pass_index = scene_state.shadow_passes.size();
	SceneState::ShadowPass shadow_pass;
	if (p_render_info) {
		p_render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_SHADOW][RS::VIEWPORT_RENDER_INFO_DRAW_CALLS_IN_FRAME] = p_instances.size();
		p_render_info->info[RS::VIEWPORT_RENDER_INFO_TYPE_SHADOW][RS::VIEWPORT_RENDER_INFO_OBJECTS_IN_FRAME] = p_instances.size();
	}
	RenderSceneDataRD scene_data;
	scene_data.cam_projection = p_projection;
	scene_data.cam_transform = p_transform;
	scene_data.view_projection[0] = p_projection;
	scene_data.z_near = 0.0;
	scene_data.z_far = p_zfar;
	scene_data.lod_distance_multiplier = p_lod_distance_multiplier;
	scene_data.dual_paraboloid_side = p_use_dp_flip ? -1 : 1;
	scene_data.opaque_prepass_threshold = 0.1;
	scene_data.time = time;
	scene_data.time_step = time_step;
	RenderDataRD render_data;
	render_data.scene_data = &scene_data;
	render_data.instances = &p_instances;
	render_data.render_info = p_render_info;
	_setup_environment(&render_data, true, Vector2(1, 1), !p_flip_y, Color(), false, p_use_pancake, shadow_pass_index);
	if (get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_DISABLE_LOD) {
		scene_data.screen_mesh_lod_threshold = 0.0;
	} else {