Regarding the sub hook-up, your NAD 3100 has a line output for the sub??? -- that's a clever feature for the stereo integrated amp. Anyway, in that case, I would try ALL of the three configurations you listed. Experiment with each one of them (each with proper subwoofer calibrations), and pick the one that sounds best to you. It's a very small investment of your time for a potentially big difference in sound quality. And you are right -- I would not choose a crossover frequency much lower (or much higher) than 80Hz.
With regard to those "hot" recordings, I am no expert on Metallica, but judging from CDs my daughter owns, yes some of the tracks sound a bit "bright" on my Hales/Axiom system (which I think is quite "accurate"). In most case, though, all you need is to lower the treble tone control a notch or two. Personally, I would never be willing to sacrifice truly "good" recordings for the "hot" ones.
