This is a BIG improvement! If you want to change the layout of a WSS/SPS-site, currently you will have to modify the site definition templateset that the site or area is based on. And still, the general sharepoint pages (in the _layouts folder) are not updated, since they’re not part of the site definition template.
But all this is a goner in SharePoint v3 (aka vNext aka ’12’). ASP.NET 2.0 masterpages are used by both the site definition template set AND the general pages. And above that, Mike Fitzmaurice explains that FrontPage 12 supports masterpages as well, which makes it a lot easier to maintain unghosted pages!