I just noticed a post on Erics site on customizing/modifying user-created web part pages, it’s worth a read for sure.
User-defined web part pages allow web designers and portal members to create isolated pages with the same basic functionality as a standard area or site page. Because they are stored in document libraries instead of the area or site collection hierarchy, they can be created, deleted, and modified without affecting portal navigation, taxonomy or search results. They serve as an effective, low-impact method for enabling user creativity.
Customizing user-defined web part pages is not quite as tricky as overhauling a complete site definition but they do present the designer with a few unique challenges.