The first two points are correct, you do get less exp (or less enemies) meaning you'll fight the end boss with 1-3 less spaces after killing everything, and yes, the Merchant now only accepts 3 items (I think).
The other two points existed before the update, meaning it's been like this for over a month. The boss you speak of isn't new, you probably just haven't seen him yet, since the boss is chosen randomly.