### 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)

skeleton->height++;
	}
	if (skeleton->transforms_texture != 0) {
		GLES3::Utilities::get_singleton()->texture_free_data(skeleton->transforms_texture);
		skeleton->transforms_texture = 0;
		skeleton->data.clear();
	}
	if (skeleton->size) {
		skeleton->data.resize(256 * skeleton->height * 4);
		glGenTextures(1, &skeleton->transforms_texture);
		glBindTexture(GL_TEXTURE_2D, skeleton->transforms_texture);
		glTexImage2D(GL_TEXTURE_2D, 0, GL_RGBA32F, 256, skeleton->height, 0, GL_RGBA, GL_FLOAT, nullptr);
		glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);
		glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
		glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
		glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
		glBindTexture(GL_TEXTURE_2D, 0);
		GLES3::Utilities::get_singleton()->texture_allocated_data(skeleton->transforms_texture, skeleton->data.size() * sizeof(float), "Skeleton transforms texture");
		memset(skeleton->data.ptrw(), 0, skeleton->data.size() * sizeof(float));
		_skeleton_make_dirty(skeleton);
	}
	skeleton->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_SKELETON_DATA);
}
void MeshStorage::skeleton_set_base_transform_2d(RID p_skeleton, const Transform2D &p_base_transform) {
	Skeleton *skeleton = skeleton_owner.get_or_null(p_skeleton);
	ERR_FAIL_NULL(skeleton);
	ERR_FAIL_COND(!skeleton->use_2d);
	skeleton->base_transform_2d = p_base_transform;
}
int MeshStorage::skeleton_get_bone_count(RID p_skeleton) const {