Without having read the article yet, I think bottom-up is legitimate in certain circumstances, as long as you prepare for it and design the system for it. See Minecraft and Kerbal Space Program.
I don't know if Minecraft is a solid example of bottom up game design when Notch worked on Wurm Online for a while and then left to make his own voxel game which turned out to be a lot like Wurm except it's popular, fun and profitable. I played Minecraft in the very early stages when it was basically just a lego building game, survival mode I would say is an extension of the building concept. So I would disagree that the gameplay is something that emerged as a result of the mechanics. One bottom-up feature of Minecraft though is multiplayer, and it has caused problems. Ideally when you build a game you should be designing it to run single player mode by connecting to a locally hosted server, then you can easily extend it and add multiplayer functionality. Notch didn't design Minecraft in this way, multiplayer has been hacked in later on and it shows. I think they're only now working to correct this early oversight, but it involves rewriting large portions of the game.
As for Kerbal Space Program, that's not an example of bottom-up game design. I've only played some earlier versions of KSP, but it seems to me that they add mechanics to facilitate gameplay, not add gameplay to give you something to do with the mechanics. When I played you could only launch craft into Kerbin orbit, now they've added a whole solar system. They certainly didn't start with a whole solar system and say to themselves "well now I guess we should add some funny little green men and their comical space program to give players something to do with this solar system"
Anyway, when I see some of the sugestions for Space Engine gameplay, I become worried, and I think I have good reason to worry.