The difference is because "is:booster" will OK the card if it has ever shown up in a booster in any set, while "in:booster" appears to be more specific to the set itself (at least, that's what it looks like after playing around a bit).
To see this, search for "Angelic Destiny" in:booster and then for "Angelic Destiny" is:booster. The first search should give you the Foundations version of the card (since that was the most recent time it was in a booster), while the second search will give you the Magic 2012 version of the card (since that was the last time it showed up as part of a standard draft booster).
As for why those twelve specific cards aren't "in:booster" for Foundations... I don't know, but if I had to hazard a guess it's because they're cards that only appear in the Starter Set and Beginner's Box and that have never appeared in a normal booster slot in any set they've been in. That feels like unintended behavior (as far as I can tell Angelic Destiny shouldn't be in:booster because it's just in the Starter Set), but I blame that on the set being weirdly massive.