### 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
scene_state.current_blend_mode = GLES3::SceneShaderData::BLEND_MODE_MIX;
	glEnable(GL_DEPTH_TEST);
	glDepthFunc(GL_LEQUAL);
	glDepthMask(GL_TRUE);
	scene_state.current_depth_test = GLES3::SceneShaderData::DEPTH_TEST_ENABLED;
	scene_state.current_depth_draw = GLES3::SceneShaderData::DEPTH_DRAW_OPAQUE;
	if (!fb_cleared) {
		glClearDepth(1.0f);
		glClear(GL_DEPTH_BUFFER_BIT);
	}
	if (!keep_color) {
		glClearBufferfv(GL_COLOR, 0, clear_color.components);
	}
	RENDER_TIMESTAMP("Render Opaque Pass");
	uint64_t spec_constant_base_flags = 0;
	{
		
		if (render_data.directional_light_count == 0) {
			spec_constant_base_flags |= SceneShaderGLES3::DISABLE_LIGHT_DIRECTIONAL;
		}
		if (render_data.environment.is_null() || (render_data.environment.is_valid() && !environment_get_fog_enabled(render_data.environment))) {
			spec_constant_base_flags |= SceneShaderGLES3::DISABLE_FOG;
		}
	}
	
	RenderListParameters render_list_params(render_list[RENDER_LIST_OPAQUE].elements.ptr(), render_list[RENDER_LIST_OPAQUE].elements.size(), reverse_cull, spec_constant_base_flags, use_wireframe);
	_render_list_template<PASS_MODE_COLOR>(&render_list_params, &render_data, 0, render_list[RENDER_LIST_OPAQUE].elements.size());
	if (draw_sky) {
		RENDER_TIMESTAMP("Render Sky");
		if (scene_state.current_depth_test != GLES3::SceneShaderData::DEPTH_TEST_ENABLED) {