The registry is safer than most standalone config systems, since writes are journalled. It's also faster, but that probably hasn't been relevant since the 80286 days (still gives a fuzzy feeling, though). It's not really hard supporting both registry and config-file support though, if you design your code properly and use a hierarchical/tree-structure configfile format like XML.
Offering two different versions shouldn't be necessary for most software, install-time (or even post-install) switching between regular and portable shouldn't be that difficult for a lot of stuff. Lots of application developers are either lazy or don't give much thought to this, though.