The author is more correct than you. Yes the FJ and Runner share suspension components the runner is 1/2' Longer and has a longer wheelbase with worse approach and departure angles. They are very similar yes but not the same.
The FJ shares more than suspension components with the 4runner. It is basically built off the same platform as the 4runner (Toyota's international LandCruiser Prado platform). Yes, wheelbase and overall length might vary slightly, but the overall design and layout is extremely similar: IFS, Solid rear axle, 4.0L V6, similar auto transmission, rear locker.
The 4th gen 4runner was different from the FJ in that it was a bit more road-oriented. The new 5th gen 4runner is basically a newer version of the FJ platform, albeit with a different body on top and slightly longer wheelbase. And I can't think of any terrain or situation that a FJ Cruiser could get through that a 5th gen 4runner couldn't (talking stock of course). Maybe they're not tit-for-tat the same, but they're close enough that it would make no sense for Toyota to introduce another FJ-type vehicle with the 5th gen 4runner still in production and with such strong sales #'s.
And back to what that author was saying, Toyota certainly didn't leave any "hole" in it's 4x4 offerings when it stopped FJ production...the most recent generation of 4runner and Tacoma have performed far better in that market than the FJ ever did.