[eluser]BrianDHall[/eluser]
I don't believe anything has changed, you are as free (or, well, not 'free') to change and extend the EE code as much as you would care to, subject only to it's own license.
I do believe this is the point of EE, that it is supposed to be easy to extend, at least partially because it is built on CodeIgniter (itself delightfully capable of extension).
Now as to using EE's authentication outside EE, that would be a question best for those especially experienced in it - it just depends how its written.