### 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
if (draw_sky || draw_sky_fog_only || environment_get_reflection_source(render_data.environment) == RS::ENV_REFLECTION_SOURCE_SKY || environment_get_ambient_source(render_data.environment) == RS::ENV_AMBIENT_SOURCE_SKY) {
			RENDER_TIMESTAMP("Setup Sky");
			Projection projection = render_data.cam_projection;
			if (render_data.reflection_probe.is_valid()) {
				Projection correction;
				correction.columns[1][1] = -1.0;
				projection = correction * render_data.cam_projection;
			}
			sky_energy_multiplier *= bg_energy_multiplier;
			_setup_sky(&render_data, *render_data.lights, projection, render_data.cam_transform, screen_size);
			if (environment_get_sky(render_data.environment).is_valid()) {
				if (environment_get_reflection_source(render_data.environment) == RS::ENV_REFLECTION_SOURCE_SKY || environment_get_ambient_source(render_data.environment) == RS::ENV_AMBIENT_SOURCE_SKY || (environment_get_reflection_source(render_data.environment) == RS::ENV_REFLECTION_SOURCE_BG && environment_get_background(render_data.environment) == RS::ENV_BG_SKY)) {
					_update_sky_radiance(render_data.environment, projection, render_data.cam_transform, sky_energy_multiplier);
				}
			} else {
				
				draw_sky = false;
			}
		}
	}
	glBindFramebuffer(GL_FRAMEBUFFER, rt->fbo);
	glViewport(0, 0, rb->width, rb->height);
	
	bool use_depth_prepass = config->use_depth_prepass;
	
	use_depth_prepass = use_depth_prepass && get_debug_draw_mode() != RS::VIEWPORT_DEBUG_DRAW_OVERDRAW;
	if (use_depth_prepass) {
		RENDER_TIMESTAMP("Depth Prepass");