I've heard that generally, the .32 caliber barrels tend to foul up quicker, and a longer .32 barrel would make it that much more difficult to drop the small powder charges intact down into the breech. Maybe the longer barrel would be better suited for a .36 caliber or larger? I really can't say since I haven't shot anything smaller than a .36 percussion myself, and all of my .36 percussions have moderate sized barrels.
But from reading posts about the popular Traditions Crockett percussion rifles with a 30 inch barrel, many folks like to use the substitute powders like 777 in them to cut down on the fouling, and which helps to make frequent swabbing less necessary. Since sub powders won't work in the flintlocks, Rusty in Italy is probably right to recommend the shorter length barrel. Plus the long, small caliber Penn. barrel will be more front heavy.
I'm sure that some people do shoot the longer barrel length .32's, but who knows how many that choose that route are happy with it? As mentioned, quick to foul is a common complaint associated with shooting the .32's. That might negate some of the accuracy of the longer barreled Penn. rifle, and its fun factor too.