Imagine you have two identical bikes, both with 100mm travel forks, 2" rise bars, same steerer length, same rise on the stem etc. But one is a 26" wheeled bike, the other a 29er.
Due to the approx (it's not quite but near enough) 3" extra height of the 29er wheel over the 26", the bars would sit 3" higher than on the 26" bike. To get over this, most 29er frames have short headtubes, which lops maybe an inch off compared to similar 26" wheeled bikes, but the bars would still sit 2" higher… Hence using flat bars to bring the bars down to a sensible height!
Got wide flat bars, low rise stem and a short (175mm) steerer on my 100mm Reba's on my Inbred 29er and it feels right. By comparison I run a 200mm steerer on my 26" wheeled hardtail, which also has 25mm more fork travel, and 1" rise bars to give me a similar position.
The Devil is in the details, as they say! 😉