### 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)

mtx.basis.rows[2][0] = dataptr[8];
					mtx.basis.rows[2][1] = dataptr[9];
					mtx.basis.rows[2][2] = dataptr[10];
					mtx.origin.z = dataptr[11];
					AABB baabb = mtx.xform(skbones[j]);
					if (first) {
						laabb = baabb;
						first = false;
					} else {
						laabb.merge_with(baabb);
					}
				}
			}
			if (laabb.size == Vector3()) {
				laabb = mesh->surfaces[i]->aabb;
			}
		} else {
			laabb = mesh->surfaces[i]->aabb;
		}
		if (i == 0) {
			aabb = laabb;
		} else {
			aabb.merge_with(laabb);
		}
	}
	mesh->aabb = aabb;
	mesh->skeleton_aabb_version = skeleton->version;
	return aabb;
}
void MeshStorage::mesh_set_shadow_mesh(RID p_mesh, RID p_shadow_mesh) {