I believe there's nothing intrinsicly wrong with a 3 bolt neck, but there'a a perceived issue due to 70's Fenders having a three bolt system and neck issues. However, if I'm recalling correctly that issue was actually down to Fender not maintaining their jigs so the worn tooling lead to mis-aligned neck joints.
I doubt Atelier would have that issue, particularly as they're Japanese.
Edit:
Just remembered, that all said, I have a mid-90s G&L with a three bolt/micro-tilt neck joint. When I got it I took it to my local guitar shop for a set-up as it was in poor condition and they removed the neck and re-attached it as it was out of alignment. BUT, it was a 17 year old instrument that hadn't been looked after especially well and is now fine four years later.