### 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)

return multimesh_owner.allocate_rid();
}
void MeshStorage::multimesh_initialize(RID p_rid) {
	multimesh_owner.initialize_rid(p_rid, MultiMesh());
}
void MeshStorage::multimesh_free(RID p_rid) {
	_update_dirty_multimeshes();
	multimesh_allocate_data(p_rid, 0, RS::MULTIMESH_TRANSFORM_2D);
	MultiMesh *multimesh = multimesh_owner.get_or_null(p_rid);
	multimesh->dependency.deleted_notify(p_rid);
	multimesh_owner.free(p_rid);
}
void MeshStorage::multimesh_allocate_data(RID p_multimesh, int p_instances, RS::MultimeshTransformFormat p_transform_format, bool p_use_colors, bool p_use_custom_data) {
	MultiMesh *multimesh = multimesh_owner.get_or_null(p_multimesh);
	ERR_FAIL_COND(!multimesh);
	if (multimesh->instances == p_instances && multimesh->xform_format == p_transform_format && multimesh->uses_colors == p_use_colors && multimesh->uses_custom_data == p_use_custom_data) {
		return;
	}