### 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)

#ifdef GLES3_ENABLED
#include "mesh_storage.h"
#include "material_storage.h"
#include "utilities.h"
using namespace GLES3;
MeshStorage *MeshStorage::singleton = nullptr;
MeshStorage *MeshStorage::get_singleton() {
	return singleton;
}
MeshStorage::MeshStorage() {
	singleton = this;
	{
		skeleton_shader.shader.initialize();
		skeleton_shader.shader_version = skeleton_shader.shader.version_create();
	}
}
MeshStorage::~MeshStorage() {
	singleton = nullptr;
	skeleton_shader.shader.version_free(skeleton_shader.shader_version);
}
RID MeshStorage::mesh_allocate() {
	return mesh_owner.allocate_rid();
}
void MeshStorage::mesh_initialize(RID p_rid) {