### 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
Sky *sky = dirty_sky_list;
	while (sky) {
		if (sky->radiance == 0) {
			sky->mipmap_count = Image::get_image_required_mipmaps(sky->radiance_size, sky->radiance_size, Image::FORMAT_RGBA8) - 1;
			
			glGenFramebuffers(1, &sky->radiance_framebuffer);
			GLenum internal_format = GL_RGB10_A2;
			glGenTextures(1, &sky->radiance);
			glBindTexture(GL_TEXTURE_CUBE_MAP, sky->radiance);
#ifdef GLES_OVER_GL
			GLenum format = GL_RGBA;
			GLenum type = GL_UNSIGNED_INT_2_10_10_10_REV;
			
			
			for (int i = 0; i < 6; i++) {
				glTexImage2D(GL_TEXTURE_CUBE_MAP_POSITIVE_X + i, 0, internal_format, sky->radiance_size, sky->radiance_size, 0, format, type, nullptr);
			}
			glGenerateMipmap(GL_TEXTURE_CUBE_MAP);
#else
			glTexStorage2D(GL_TEXTURE_CUBE_MAP, sky->mipmap_count, internal_format, sky->radiance_size, sky->radiance_size);
#endif
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_MIN_FILTER, GL_LINEAR_MIPMAP_LINEAR);
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_BASE_LEVEL, 0);
			glTexParameteri(GL_TEXTURE_CUBE_MAP, GL_TEXTURE_MAX_LEVEL, sky->mipmap_count - 1);