### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

while (skeleton_dirty_list) {
		Skeleton *skeleton = skeleton_dirty_list;
		if (skeleton->size) {
			glBindTexture(GL_TEXTURE_2D, skeleton->transforms_texture);
			glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, 256, skeleton->height, 0, GL_RGBA, GL_FLOAT, skeleton->data.ptr());
			glBindTexture(GL_TEXTURE_2D, 0);
		}
		skeleton_dirty_list = skeleton->dirty_list;
		skeleton->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_SKELETON_BONES);
		skeleton->version++;
		skeleton->dirty = false;
		skeleton->dirty_list = nullptr;
	}
	skeleton_dirty_list = nullptr;
}
void MeshStorage::skeleton_update_dependency(RID p_skeleton, DependencyTracker *p_instance) {
	Skeleton *skeleton = skeleton_owner.get_or_null(p_skeleton);
	ERR_FAIL_COND(!skeleton);
	p_instance->update_dependency(&skeleton->dependency);
}
#endif