To me the difference between high flange wheels built 3x and low flange wheels built 3x are minimal or non-existent as far as ride comfort. There is a noticeable difference in terms of stability around corners or on a velodrome with the high flange wheels taking the advantage. In general I'd say a high flange wheel built up 3x is equivalent to a low flange wheel built up 2x in terms of comfort. If the spoke lengths are the same the ride should be similarly comfortable. For comfort, I go for a longer wheelbase with slacker angles, a touring saddle and one size up tires. If those things are in play, high flange wheels won't make a lick of difference.
Garth Libre in Miami Fl USA