The reason is simple, if trivial.
If I'm going to have several domains on the account, I don't want loads of directories in the home directory. I'd rather have them all in a subdirectory called 'www'. It would be a shade easier for me to manage that way. It would also mean the paths match my local machine.
Anyway, it wasn't essential but the functionality was there on the control panel, so I've done it now.
I'd be interested to know if there's a reason why I should go back to the default settings, and also if this can be considered a bug (albeit a minor one).