### 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
pipeline_version = SceneShaderForwardClustered::PIPELINE_VERSION_COLOR_PASS;
			} break;
			case PASS_MODE_SHADOW:
			case PASS_MODE_DEPTH: {
				pipeline_version = p_params->view_count > 1 ? SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_MULTIVIEW : SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS;
			} break;
			case PASS_MODE_SHADOW_DP: {
				ERR_FAIL_COND_MSG(p_params->view_count > 1, "Multiview not supported for shadow DP pass");
				pipeline_version = SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_DP;
			} break;
			case PASS_MODE_DEPTH_NORMAL_ROUGHNESS: {
				pipeline_version = p_params->view_count > 1 ? SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_NORMAL_AND_ROUGHNESS_MULTIVIEW : SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_NORMAL_AND_ROUGHNESS;
			} break;
			case PASS_MODE_DEPTH_NORMAL_ROUGHNESS_VOXEL_GI: {
				pipeline_version = p_params->view_count > 1 ? SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_NORMAL_AND_ROUGHNESS_AND_VOXEL_GI_MULTIVIEW : SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_NORMAL_AND_ROUGHNESS_AND_VOXEL_GI;
			} break;
			case PASS_MODE_DEPTH_MATERIAL: {
				ERR_FAIL_COND_MSG(p_params->view_count > 1, "Multiview not supported for material pass");
				pipeline_version = SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_MATERIAL;
			} break;
			case PASS_MODE_SDF: {
				
				ERR_FAIL_COND_MSG(p_params->view_count > 1, "Multiview not supported for SDF pass");
				pipeline_version = SceneShaderForwardClustered::PIPELINE_VERSION_DEPTH_PASS_WITH_SDF;
			} break;
		}
		PipelineCacheRD *pipeline = nullptr;
		if constexpr (p_pass_mode == PASS_MODE_COLOR) {
			pipeline = &shader->color_pipelines[cull_variant][primitive][pipeline_color_pass_flags];
		} else {