### 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)

MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
	ERR_FAIL_COND_V(!multimesh, Transform3D());
	ERR_FAIL_INDEX_V(p_index, multimesh->instances, Transform3D());
	ERR_FAIL_COND_V(multimesh->xform_format != RS::MULTIMESH_TRANSFORM_3D, Transform3D());
	_multimesh_make_local(multimesh);
	Transform3D t;
	{
		const float *r = multimesh->data_cache.ptr();
		const float *dataptr = r + p_index * multimesh->stride_cache;
		t.basis.rows[0][0] = dataptr[0];
		t.basis.rows[0][1] = dataptr[1];
		t.basis.rows[0][2] = dataptr[2];
		t.origin.x = dataptr[3];
		t.basis.rows[1][0] = dataptr[4];
		t.basis.rows[1][1] = dataptr[5];
		t.basis.rows[1][2] = dataptr[6];
		t.origin.y = dataptr[7];
		t.basis.rows[2][0] = dataptr[8];
		t.basis.rows[2][1] = dataptr[9];
		t.basis.rows[2][2] = dataptr[10];
		t.origin.z = dataptr[11];
	}
	return t;
}
Transform2D MeshStorage::multimesh_instance_get_transform_2d(RID p_multimesh, int p_index) const {