I'm not sure you are talking about two different things. Every single external USB and/or Firewire harddrive that I've seen are nothing more than standard hard drives (IDE) installed inside a case with a IDE-to-Firewire (or USB) bridge.
So if I understand you correctly, there are no differences, they are one in the same. Sometimes you can get a better price buying an external drive (hard drive inside an enclosure) vs. buying an enclosure and then inserting a hard drive.
The benefit of putting your own hard drive into an enclosure is you get to pick the exact make and model of hard drive; whereas, with pre-builts, you get whatever drive they use.