I'm skeptical of that. There are a lot of things to do with garrisons that favor an alt army. Also, the things you get from pet stones don't really lead to any kind of "progression" and can all be gotten in unlimited quantities elsewhere. Also, everything you can buy with them is BoA and the most expensive thing is only 15 charms, so it would be a pretty superficial gating.
My best guess, though I don't think it's a very good one, would be it has something to do with how big a hassle it is to run around to the pet trainers without flying and parking alts at them. Hopefully it's just a poor decision that nobody looked closely at and they'll fix it before long.