### 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 *skeleton = skeleton_owner.get_or_null(p_skeleton);
	ERR_FAIL_COND(!skeleton);
	ERR_FAIL_INDEX(p_bone, skeleton->size);
	ERR_FAIL_COND(!skeleton->use_2d);
	float *dataptr = skeleton->data.ptrw() + p_bone * 8;
	dataptr[0] = p_transform.columns[0][0];
	dataptr[1] = p_transform.columns[1][0];
	dataptr[2] = 0;
	dataptr[3] = p_transform.columns[2][0];
	dataptr[4] = p_transform.columns[0][1];
	dataptr[5] = p_transform.columns[1][1];
	dataptr[6] = 0;
	dataptr[7] = p_transform.columns[2][1];
	_skeleton_make_dirty(skeleton);
}
Transform2D MeshStorage::skeleton_bone_get_transform_2d(RID p_skeleton, int p_bone) const {