### 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)

glBindBuffer(GL_ARRAY_BUFFER, multimesh->buffer);
					for (uint32_t i = 0; i < visible_region_count; i++) {
						if (multimesh->data_cache_dirty_regions[i]) {
							GLint offset = i * region_size;
							GLint size = multimesh->stride_cache * (uint32_t)multimesh->instances * (uint32_t)sizeof(float);
							uint32_t region_start_index = multimesh->stride_cache * MULTIMESH_DIRTY_REGION_SIZE * i;
							glBufferSubData(GL_ARRAY_BUFFER, offset, MIN(region_size, size - offset), &data[region_start_index]);
						}
					}
					glBindBuffer(GL_ARRAY_BUFFER, 0);
				}
				for (uint32_t i = 0; i < data_cache_dirty_region_count; i++) {
					multimesh->data_cache_dirty_regions[i] = false;
				}
				multimesh->data_cache_used_dirty_regions = 0;
			}
			if (multimesh->aabb_dirty && multimesh->mesh.is_valid()) {
				_multimesh_re_create_aabb(multimesh, data, visible_instances);
				multimesh->aabb_dirty = false;
				multimesh->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_AABB);
			}
		}
		multimesh_dirty_list = multimesh->dirty_list;
		multimesh->dirty_list = nullptr;
		multimesh->dirty = false;
	}
	multimesh_dirty_list = nullptr;
}
RID MeshStorage::skeleton_allocate() {