I guess I'd just define "extra limb" really simple: More than you currently have (not what you originally should have had). So if you're missing an arm, getting it back via a spell is increasing mass. The lower level spells on that list are really intended to just alter the outward appearance of your existing body, not change the size or shape of it. So the 5th level,Change to Kind; That means you're changing to something that is essentially the same form as you, but with a different appearance. So, Elf to Human, Human to Lizard Man and so on. But not Hobbit to Human or Elf to Hobbit. That's a mass change that this spell does not cover. Enlarge (2nd level) takes your current form and just makes it bigger, like blowing up a picture. You don't alter it, you just make it bigger. But when you get to the 11th level spell it says you can take ANY organic form with up to a 200% size difference... that's when I'd let you get your arm back via the spell.
But I am all for Spell Mastery and, yeah, I think I'd allow that in this case, particularly in the case of the "Enlarge" spell. The more creative we can be as players (without getting into the absurd - heh, fireballs, but anyhow...) the more fun the game IMO.