Argh, you used a flawless stone on the alliance balloon? That was a bit of a waste since it can't even battle.
Not sure it's even possible to get 100% rare on warcraftpets - I stoned my last unique pet a few weeks ago but my profile shows 98.5% rare because of the aforementioned non-combat pets.
I wouldn't say it's a waste to stone the non combat pets to rare if that's what you want to do (personally I like my wall of blue... except that DAMN SKY LANTERN!)
And you are correct, you cannot get 100% rare on WCP if you have the non combat pets in your collection due to the armory. But I'd rather see it that way than see them all get flagged to rare since I doubt most people bother stoning theirs.