honda doesnt make just undersquare engines. the 3.0, and new civic si engines are sqaure, both are 3.39x3.39. and undersquare engines make more high rpm horsepower, while oversquare engines make more low end torque. (that is if im not getting my terminology confused by the article you posted)

engine with bigger borexstroke requires more duration than lift, making more low-end torque

engine with smaller borexstroke needs more lift so more air can enter quicker, making more hp on the top-end.