I doubt there's one single "best practice" for this kind of thing; it is probably more dependent on your own preference and working environment. A script offers more overhead, but also potentially more control and error checking; direct registry edits are likely quicker and easier to view in the console, and you don't need to worry about scripting language compatibility on legacy hardware (some of us still have Windows 2000 kicking around).
I've never been shy about modifying the registry directly, as the BL console makes it a fairly straightforward and repeatable process. In this case, I suppose it is acting as a stand-in for a script of some sort.
Your mileage may vary, as is said.