### 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
c.push_back(cc);
			if (rb_data.is_valid()) {
				c.push_back(Color(0, 0, 0, 0)); 
				c.push_back(Color(0, 0, 0, 0)); 
			}
		}
		RenderListParameters render_list_params(render_list[RENDER_LIST_OPAQUE].elements.ptr(), render_list[RENDER_LIST_OPAQUE].element_info.ptr(), render_list[RENDER_LIST_OPAQUE].elements.size(), reverse_cull, PASS_MODE_COLOR, color_pass_flags, rb_data.is_null(), p_render_data->directional_light_soft_shadows, rp_uniform_set, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_WIREFRAME, Vector2(), p_render_data->scene_data->lod_distance_multiplier, p_render_data->scene_data->screen_mesh_lod_threshold, p_render_data->scene_data->view_count);
		_render_list_with_threads(&render_list_params, color_framebuffer, keep_color ? RD::INITIAL_ACTION_KEEP : RD::INITIAL_ACTION_CLEAR, will_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, depth_pre_pass ? (continue_depth ? RD::INITIAL_ACTION_CONTINUE : RD::INITIAL_ACTION_KEEP) : RD::INITIAL_ACTION_CLEAR, will_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, c, 1.0, 0);
		if (will_continue_color && using_separate_specular) {
			
			RD::get_singleton()->draw_list_begin(rb_data->get_specular_only_fb(), RD::INITIAL_ACTION_CONTINUE, RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, RD::FINAL_ACTION_CONTINUE);
			RD::get_singleton()->draw_list_end();
		}
	}
	RD::get_singleton()->draw_command_end_label();
	if (debug_voxelgis) {
		
		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 cm = (dc * p_render_data->scene_data->cam_projection) * Projection(p_render_data->scene_data->cam_transform.affine_inverse());
		RD::DrawListID draw_list = RD::get_singleton()->draw_list_begin(color_only_framebuffer, RD::INITIAL_ACTION_CONTINUE, will_continue_color ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ, RD::INITIAL_ACTION_CONTINUE, will_continue_depth ? RD::FINAL_ACTION_CONTINUE : RD::FINAL_ACTION_READ);
		RD::get_singleton()->draw_command_begin_label("Debug VoxelGIs");
		for (int i = 0; i < (int)p_render_data->voxel_gi_instances->size(); i++) {
			gi.debug_voxel_gi((*p_render_data->voxel_gi_instances)[i], draw_list, color_only_framebuffer, cm, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_VOXEL_GI_LIGHTING, get_debug_draw_mode() == RS::VIEWPORT_DEBUG_DRAW_VOXEL_GI_EMISSION, 1.0);
		}
		RD::get_singleton()->draw_command_end_label();
		RD::get_singleton()->draw_list_end();
	}