### 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 (debug_sdfgi_probes) {
		
		bool will_continue_color = (can_continue_color || draw_sky || draw_sky_fog_only);
		bool will_continue_depth = (can_continue_depth || draw_sky || draw_sky_fog_only);
		Projection dc;
		dc.set_depth_correction(true);
		Projection cms[RendererSceneRender::MAX_RENDER_VIEWS];
		for (uint32_t v = 0; v < p_render_data->scene_data->view_count; v++) {
			cms[v] = (dc * p_render_data->scene_data->view_projection[v]) * Projection(p_render_data->scene_data->cam_transform.affine_inverse());
		}
		_debug_sdfgi_probes(rb, color_only_framebuffer, p_render_data->scene_data->view_count, cms, will_continue_color, will_continue_depth);
	}
	if (draw_sky || draw_sky_fog_only) {
		RENDER_TIMESTAMP("Render Sky");
		RD::get_singleton()->draw_command_begin_label("Draw Sky");
		RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(color_only_framebuffer, RD::INITIAL_ACTION_CONTINUE, can_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, can_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ);
		sky.draw_sky(draw_list, rb, p_render_data->environment, color_only_framebuffer, time, sky_energy_multiplier);
		RD::get_singleton()->draw_list_end();
		RD::get_singleton()->draw_command_end_label();
	}
	if (rb.is_valid() && !can_continue_color && rb->get_msaa_3d() != RS::VIEWPORT_MSAA_DISABLED) {
		
		for (uint32_t v = 0; v < rb->get_view_count(); v++) {
			RD::get_singleton()->texture_resolve_multisample(rb_data->get_color_msaa(v), rb->get_internal_texture(v));
		}
		if (using_separate_specular) {
			for (uint32_t v = 0; v < rb->get_view_count(); v++) {
				RD::get_singleton()->texture_resolve_multisample(rb_data->get_specular_msaa(v), rb_data->get_specular(v));
			}
		}