That website doesn't make me feel confident, so I did some research:
http://www.usmle.org/pdfs/Changes_to_USMLE_2014-2015_handout_FINAL.pdf
Basically, if you register for Step 3 after July 31, then you can take it on two non-consecutive days (it is already two days), but it will still be scored as one exam. And if you take the exam after November 1,2014, you're going to have to wait until April to get your score. It does not sound like they're going to make you pay for two separate exams, though the price of Step 3 may very well go up.
That really incentivizes me to take it really, really early in intern year. Which is probably for the best anyway, since I'm not going to be treating adults anymore.