One has to wonder why Littlepip's stable seems to be the only one that wasn't subjected to terrible experiments that had Gone Horribly Right. Then you realize that her Stable is only the second one ever built, and most likely was constructed for the actual purpose of protection when Scootaloo first started constructing them.
First, only one "experiment" that we've seen actually contributed to the Stable's downfall. This isn't Vault-Tec. None of the experiments were really "terrible" Secondly, Stable 2 was intended from the start to be a control stable, one without any experiment, and it wasn't the only one.
Your point is rendered kind of moot when you consider Project Horizons.