I dont think it would look like a 2 stroke then and i think it would affect performace to as the pipes would be rerouted... I like the side by side slightly diffrent length look much more that a 4 stoke under seat job...although my fav chocolate engine yam is a reverse cylinder 3ma it has pipes under seat and looks cool.
this one in fact, actually the more i look at it......MMMM ebay
http://www.bikepics.com/pictures/076209/