### 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 (scene_state.instance_data[p_render_list].size() > 0) {
		if (scene_state.instance_buffer[p_render_list] == RID() || scene_state.instance_buffer_size[p_render_list] < scene_state.instance_data[p_render_list].size()) {
			if (scene_state.instance_buffer[p_render_list] != RID()) {
				RD::get_singleton()->free(scene_state.instance_buffer[p_render_list]);
			}
			uint32_t new_size = nearest_power_of_2_templated(MAX(uint64_t(INSTANCE_DATA_BUFFER_MIN_SIZE), scene_state.instance_data[p_render_list].size()));
			scene_state.instance_buffer[p_render_list] = RD::get_singleton()->storage_buffer_create(new_size * sizeof(SceneState::InstanceData));
			scene_state.instance_buffer_size[p_render_list] = new_size;
		}
		RD::get_singleton()->buffer_update(scene_state.instance_buffer[p_render_list], 0, sizeof(SceneState::InstanceData) * scene_state.instance_data[p_render_list].size(), scene_state.instance_data[p_render_list].ptr(), RD::BARRIER_MASK_RASTER);
	}
}
void RenderForwardClustered::_fill_instance_data(RenderListType p_render_list, int *p_render_info, uint32_t p_offset, int32_t p_max_elements, bool p_update_buffer) {
	RenderList *rl = &render_list[p_render_list];
	uint32_t element_total = p_max_elements >= 0 ? uint32_t(p_max_elements) : rl->elements.size();
	scene_state.instance_data[p_render_list].resize(p_offset + element_total);
	rl->element_info.resize(p_offset + element_total);
	if (p_render_info) {
		p_render_info[RS::VIEWPORT_RENDER_INFO_OBJECTS_IN_FRAME] += element_total;
	}
	uint64_t frame = RSG::rasterizer->get_frame_number();
	uint32_t repeats = 0;
	GeometryInstanceSurfaceDataCache *prev_surface = nullptr;
	for (uint32_t i = 0; i < element_total; i++) {
		GeometryInstanceSurfaceDataCache *surface = rl->elements[i + p_offset];
		GeometryInstanceForwardClustered *inst = surface->owner;
		SceneState::InstanceData &instance_data = scene_state.instance_data[p_render_list][i + p_offset];
		if (inst->prev_transform_dirty && frame > inst->prev_transform_change_frame + 1 && inst->prev_transform_change_frame) {
			inst->prev_transform = inst->transform;
			inst->prev_transform_dirty = false;