Not sure if this is a bug or a feature, hence, this thread.
On ST2, when your selection included a line break and you hit Ctrl+F or Ctrl+H to either search of replace, the "within selection" option was turned on, automatically. This feature appears to have been lost, broken, or removed on ST3.
If it's broken or lost, this is plead to the devs to fix it or add it - I use ST3 on a daily basis (I know I'm not supposed to be working with it, but it's just too tempting), and other than goto-anything, this is probably the feature I used the most, and I sorely miss it.
If it has been removed, this is a plead to the product owners to splash some cool water on their faces and regain control of their senses. I have nothing but the uttermost admiration for the ST team in general, but, guys, I'm dead serious - this killer feature is a must have.