The author of the 'Do This First' article is Dan John, an exceptional strength coach who actually has considerable connectivity to the CrossFit world.
The kipping vs conventional debate actually doesn't exist in CF-land. They do both. You can consider one to be a 'pure strength' movement and the other to be a 'skill-strength' movement along the lines of certain kettlebell exercises.
(Disclaimer: I have no stock in CF, do not train using their 'conceptual model' and I have specialized goals that would not be adequately met using the CF structure).
If you look at any one CF workout, you might easily conclude that CF people 'flip tires' do 'kipping pull-ups' perform 'box jumps' or whatever else it was that you saw and that is 'all they do'.
There are a couple of problems with this type of analysis. The first is that unless you're watching a CF group who follows the 'Workout of the Day' or (WOD) as posted on the CF website to the letter... you may not be watching a CF workout. The 'official' CF workouts possess considerable variety and will (eventually) address absolute strength and power development. But it will be addressed in a way that does not prioritize it any more than endurance or metabolic conditioning is prioritized. The CF follower wants 'everything' as opposed to any one thing.
But here's the thing, there are a bunch of 'licensed' CF coaches who do not follow the WOD. What they're doing is using the CF 'principles' and cooking up their own workouts. So are they doing CF? They believe that they are. But we're now talking maybe over a thousand people across the country doing their own 'interpretation' of CF. That makes CF a lot harder to quantify.
Sometimes these workout modifications are logistics-related. For example. Progressive FORCE Concepts (PFC) runs a CF gym in Las Vegas. But at the moment they do not have any Concept 2 rowing machines. These machines are a CF staple. Further, many PFC CF sessions take place out in the 'field' where equipment is minimal and frequently improvised. So if you saw THOSE workouts you might conclude that CF people work out with ammo cans full of sand, a couple kettle bells, and wear helmets and rucksacks while training.
And while those 'field' workouts might look random, the person who designed them will get great results from them. And this is because that person is a great fitness coach, not because a weekend CF certification taught him everything he needs to know.
CF is like anything else. I can show you some CF guys who would absolutely kill you and I can show you some CF punks. It is still all about the individual, and moreover, it is really about the individual CF coach. I know some brilliant CF coaches, who know and do much more than what is espoused within the confines of the CF model. And I've met some CF coaches that know only what CF has told them.
In the end this almost becomes a JKD-like debate. And the debate would become meaningless if everyone would simply do what Jim McCann says and "Train like a madman".