1) Hasn't been the case for years. +R is actually preferred these days if you ask most people. But you're right, the BenQ isn't your drive if -R is your trade (at least not with current BSKB fw).
2) I've only used my 1620 & 1640 in external, USB 2.0 cases. Never a problem. So not an issue either way (I think it's more an issue of having the right case than the right drive).
3) This one's a tough one, but if you look at the NEC forum, specifically the L&D fw threads, you will see what's in my view lots more people "testing beta software" and "wasting discs." They enjoy it, but I went with BenQ specifically because I don't want to deal with that. So I actually see the BenQ as having the desired out-of-box functionality that you attribute to the NEC!
The burn quality of my 3520 was complete crap on my TY T02 +R discs compared to my 1620, so unless the 3540 is wildly different I can't see it beating a 1640 in PIF on +R. -R may be a diff. story, I wouldn't know either way cuz I don't use them.