### 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)

Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, AABB());
	if (mesh->custom_aabb != AABB()) {
		return mesh->custom_aabb;
	}
	Skeleton *skeleton = skeleton_owner.get_or_null(p_skeleton);
	if (!skeleton || skeleton->size == 0 || mesh->skeleton_aabb_version == skeleton->version) {
		return mesh->aabb;
	}
	
	AABB aabb;
	for (uint32_t i = 0; i < mesh->surface_count; i++) {
		AABB laabb;
		if ((mesh->surfaces[i]->format & RS::ARRAY_FORMAT_BONES) && mesh->surfaces[i]->bone_aabbs.size()) {
			int bs = mesh->surfaces[i]->bone_aabbs.size();
			const AABB *skbones = mesh->surfaces[i]->bone_aabbs.ptr();
			int sbs = skeleton->size;
			ERR_CONTINUE(bs > sbs);
			const float *baseptr = skeleton->data.ptr();
			bool first = true;
			if (skeleton->use_2d) {
				for (int j = 0; j < bs; j++) {
					if (skbones[j].size == Vector3(-1, -1, -1)) {
						continue; 
					}
					const float *dataptr = baseptr + j * 8;