The handlebar on a 29er will always be higher than on a 26 (unless you go with negative-rise stems and upside-down riser bars or other extreme stuff).
This simply isn't true. The only thing that will always be higher for a given amount of fork length is the bottom of the head tube. 29ers designed by people who are paying attention will have substantially shorter head tubes than the equivalent 26in bike. If we're talking suspension forks, then 29ers usually have less travel than 26in bikes pitched at the same kind of riding at the same kind of point. If you look at manufacturers that have 26 and 29in versions of the same bike, if the 26in one is 120mm travel the 29 is likely to be 100mm. And since most modern 26in bikes have riser bars, some stem rise and a bunch of spacers under them, you don't need a very extreme front end setup to get a 29er bar down to the same height. Usually just a flat bar does it. The only 29ers I've seen with neg-rise stems are XC race bikes for short people.
Remember that while a 29in wheel usually does measure about 29in, most modern "26in" wheels are more like 27, so there's not that much height to lose
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