I don't think you are missing anything.
I'm the last person that would discourage drilling into a kayak. My yak has two through hull fittings below the waterline. I've taken my fair share of naysayer abuse for those. This mod is one I am a bit more cautious about for one reason- If the the check valve sticks open, there is the possibility that you now have an open hose that will allow water to flow directly into the hull of the yak. We only sit a few inches above the water, so water coming into a fitting above the waterline wouldn't be that difficult. Ever find water in your flush mount rod holders on a choppy day? Even the best check valve won't seal 100% of the water out. Things also corrode fairly easily on kayaks due to us getting wetter in the surf & how close we sit to the water. Anything electrical- from bait pumps, fuses, batteries, to fishfinder connections are prone to corrosion, so there is also the real possibility that the pump won't turn on after water is in the hull. Yes, all of that happening is a "worst case scenario", but I don't think it is too far fetched. If you do this mod, I'd still carry hand pump as a back-up to your back-up just for a little peace of mind.
I'm sure you will never need the electric bilge, or the hand pump. The only time I've ever used my hand pump on the water was to lend it to another kayaker that had taken on water. I apologize if my post above came across as negative. I love guys that push the envelope in regard to rigging up their yaks.
In regard to you original question- most bilge pumps will have a 3/4" hose outlet connection, which will require a 1" hole in the kayak. The fitting looks like this:
http://www.westmarine.com/webapp/wcs...1#.ULBQ-kSRvW8
In regard to how to actually rig it up, I would take Jim's advice in post #8 on the link you provided.
Good luck, let us know how it goes. We want to see pics of this thing all rigged up!
