RE #1) The Boss is safer to drive? This is a Mustang race car, not a Volvo station wagon. Faster? The R is roughly 700 lbs lighter than the Boss and has a very similar (actual) power rating. Creature comforts? Buy a new BMW or Porsche like every other middle-aged Orthodontist in the world.
RE #2) I'd be willing to bet you still wouldn't be eager to try and reenact any Dukes of Hazzard scenes in what is also a $45k car. Although this is purely hypothetical, since I presume that like most of the other bottom feeders on this site, the Ford Aspire is an aspirational car to you.
RE #3) Again, this is a purpose built race car and not some Camry with a bunch of bright red "S" logos glued to it. Something tells me you have a Consumers Reports subscription that you religiously renew every year. Totally different set of priorities in this segment. You also forgot to criticize it's lack of cup holders compared to the 2012 Honda Odyssey.
Bottom line- they both have their own interpretations of Mustang performance philosophy and neither one is totally right or wrong. I wouldn't mind either one in my garage, but I must admit I do have a soft spot for the 2000 (IRS FTW). I personally find the retro theme a bit played out; it's been going on for so long they're probably going to come out with a new retro-retro version of the 2005 Mustang soon. For that matter, which is more subtle; a two foot tall spoiler or huge side graphics? I digress...
FYI; the price is indeed fair for a 2000 Cobra R in mint condition.