Is per-word pricing actually how writers still get paid, or is this site just reporting that as a common metric? Most of the freelance writers I've spoken to have gotten paid either per-piece (lots of blog shadow writing), or per-hour.
It's also how I used to be paid as a jobbing IT reviewer/columnist/journalist in the British newsstand computer trade press (caveat: I switched to writing novels full-time in 2005).
I've never known a publication to count the words exactly, once the story is delivered. A finished piece of 970 words or 1,050 words will get paid the standard rate for 1,000 words, without any adjustments.
Hope that helps.