I wouldn't say the handsewn is inherently higher quality. The resulting look is slightly different.
I have a pair of Alden shell tassel loafers (from shoe mart factory seconds, with possibly fewer imperfections than my first quality models -- that's a tale for another time), and I like the machine stitch on the apron. It's a bit "neater" and that makes it a bit dressier than the handsewn, which works for what I wear them for. Of course, if you are going for something more casual, then that won't be an issue. I think there is a place for both.