There's actually a 3rd process that is viable now: download the Android froyo 2.2 and install it to an extra SD card ... then boot from that. It won't root your Nook, but you'll be able to have all the fun of an android tablet. I was running it yesterday, and it was quite usable.
When you are done, power down the Nook, pop out the 2.2 SD card, pop in your regular card, and reboot > presto, you are at your regular nook!
Although I love my rooted nook, and the autonooter process is very easy, this new method allows you to experience a rooted nook, w/o rooting!
If you are curious, I'll provide a link.