So is the online gamestop tracker for the "New" collector's edition a reliable way to track one down or is it totally random whether or not a store has it?
It's a good indicator of which stores HAD it in stock new, but whether it is still available is extremely YMMV. It could be:
a. Yes, it's still there and complete
b. Yes, it's still there but on hold for someone else
c. No, somebody already bought it today (I don't think their inventory system updates until the next morning)
d. No, they already gutted or sold it without changing their "NEW" inventory count