### 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
material_storage->shaders.sky_shader.version_set_uniform(SkyShaderGLES3::TIME, time, shader_data->version, SkyShaderGLES3::MODE_CUBEMAP);
		material_storage->shaders.sky_shader.version_set_uniform(SkyShaderGLES3::PROJECTION, cm.columns[2][0], cm.columns[0][0], cm.columns[2][1], cm.columns[1][1], shader_data->version, SkyShaderGLES3::MODE_CUBEMAP);
		material_storage->shaders.sky_shader.version_set_uniform(SkyShaderGLES3::LUMINANCE_MULTIPLIER, p_luminance_multiplier, shader_data->version, SkyShaderGLES3::MODE_CUBEMAP);
		glBindVertexArray(sky_globals.screen_triangle_array);
		glViewport(0, 0, sky->radiance_size, sky->radiance_size);
		glBindFramebuffer(GL_FRAMEBUFFER, sky->radiance_framebuffer);
		for (int i = 0; i < 6; i++) {
			Basis local_view = Basis::looking_at(view_normals[i], view_up[i]);
			material_storage->shaders.sky_shader.version_set_uniform(SkyShaderGLES3::ORIENTATION, local_view, shader_data->version, SkyShaderGLES3::MODE_CUBEMAP);
			glFramebufferTexture2D(GL_FRAMEBUFFER, GL_COLOR_ATTACHMENT0, GL_TEXTURE_CUBE_MAP_POSITIVE_X + i, sky->raw_radiance, 0);
			glDrawArrays(GL_TRIANGLES, 0, 3);
		}
		if (update_single_frame) {
			for (int i = 0; i < max_processing_layer; i++) {
				_filter_sky_radiance(sky, i);
			}
		} else {
			_filter_sky_radiance(sky, 0); 
		}
		sky->processing_layer = 1;
		sky->baked_exposure = p_luminance_multiplier;
		sky->reflection_dirty = false;
	} else {
		if (sky_mode == RS::SKY_MODE_INCREMENTAL && sky->processing_layer < max_processing_layer) {
			_filter_sky_radiance(sky, sky->processing_layer);
			sky->processing_layer++;
		}
	}
}
Vector3 importance_sample_GGX(Vector2 xi, float roughness4) {