It's because Dark has excellant nuetral coverage. Not sure on why it says secondary stab either though, as Greninja gets stab on everything.
That makes sense, perhaps the analysis should state that, though I still think something not weak to one of the other major attacks greninja has (i.e. stuff on set + Grass Knot/Extrasensory) would be a better example to use than starmie - one of the more popular ghosts that Dark Pulse handles perhaps?
On the topic of grass knot though, it does 2HKO Azumarill (252 SpA Life Orb Protean Greninja (Move 1) vs. 252 HP / 0 SpD Azumarill: 265-312 (65.5 - 77.2%), Move 1 is a 60BP Grass Move as PS!'s calc doesn't seem to like grass knot), so if you predict the switch in you can take that out, which might be worth mentioning seeing as Azumarill resists every other common move (Extrasensory hits it neutral but is rare and HP Electric, if anyone is running that still, hits for the same BP but leaves you neutral to aqua jet/waterfall) and OHKO's with Play Rough (even if you're neutral to it from protean, it still deals 96.5 - 113.6%, a OHKO after a single round of LO Recoil, unboosted), and is thus mentioned as a counter - grass knot at least means Azumarill will not be able to mindlessly switch into every greninja (as plenty are carrying it at the moment it might be worth mentioning, I dunno).
Shame it doesn't do slightly more to Rotom-W, as while it lets you resist both its STABs, Rotom-W+LO Recoil will generally kill you even if you can do any kind of damage to it (which basically requires also running Dark Pulse).
Not enough for a slash but perhaps it warrants mentioning, idk.