### Godot version

v4.2.beta1.official [b1371806a]

### System information

Ubuntu 22.04.3 LTS 22.04 - X11 - GLES3 (Compatibility) - AMD Radeon RX 560 Series (polaris11, LLVM 15.0.7, DRM 3.42, 5.15.0-88-generic) () - AMD Ryzen 3 1200 Quad-Core Processor (4 Threads)

### Issue description

![image](https://github.com/godotengine/godot/assets/1330325/7a986599-5a68-42a4-beb1-5d3b4bf7db6b)
![image](https://github.com/godotengine/godot/assets/1330325/e8b8546b-b47b-4add-9567-7f70709ab03c)

Culling 3D goes bellow 60 fps even with just about 50 simple animated models. With v4.2.dev6.official [57a6813bb] many more models can be spawned without fps drop. However, both versions do show high cpu usage for culling 3D. Without animations there's barely any usage.

### Steps to reproduce

Spawn models with animation with the Compatibility renderer.

### Minimal reproduction project

[CullMRP.zip](https://github.com/godotengine/godot/files/13400514/CullMRP.zip)

MeshInstance *mi = mesh_instance_owner.get_or_null(p_rid);
	_mesh_instance_clear(mi);
	mi->mesh->instances.erase(mi->I);
	mi->I = nullptr;
	mesh_instance_owner.free(p_rid);
}
void MeshStorage::mesh_instance_set_skeleton(RID p_mesh_instance, RID p_skeleton) {
	MeshInstance *mi = mesh_instance_owner.get_or_null(p_mesh_instance);
	if (mi->skeleton == p_skeleton) {
		return;
	}
	mi->skeleton = p_skeleton;
	mi->skeleton_version = 0;
	mi->dirty = true;
}
void MeshStorage::mesh_instance_set_blend_shape_weight(RID p_mesh_instance, int p_shape, float p_weight) {
	MeshInstance *mi = mesh_instance_owner.get_or_null(p_mesh_instance);
	ERR_FAIL_NULL(mi);
	ERR_FAIL_INDEX(p_shape, (int)mi->blend_weights.size());
	mi->blend_weights[p_shape] = p_weight;
	mi->dirty = true;
}
void MeshStorage::_mesh_instance_clear(MeshInstance *mi) {