the gearing between the 2 boxes is virtually the same, the 6th speed has a slightly shorter final drive meaning gears 1 to 5 are slightly lower, 5th for instance on the 5 speed box is 25.2mph per 1000rpm while on the 6 speed box it's about 24.5mph per 1000rpm, 6th gear is about 27.5mph per 1000rpm so it's slightly more relaxed at motorway speeds
having the 6 speed box does make the car more desireable though so if you can find one with that box then go for it
if you want the exact ratio's for each i can dig them up for you, just let me know