The bubble on the top may have been one of the rare defects, and instead of trashing it, they put it on display. Can't say, wasn't there.
But, as to the caulking, the reason it's done is to prevent dirty mop water, misses, dribbles, etc., from getting underneath the toilet. Most places REQUIRE it to be caulked for these reasons, but most only do it around the front of the toilet, leaving the rear open. If the toilet is installed properly (this also means it doesn't rock), there's little chance of it breaking the seal and leaking.