I read someplace that some people do not recommend putting SharePoint multiples web applications onto the same port, e.g., the traditional http: port 80.
Here's some history. My original plan was to host my WSS internet web applications on a custom port and extend to port 80 for general consumption, and that was my initial set up. But my hosting provider keeps most ports locked down which meant I could see it just fine from a browser on the server, but not from the internet cloud. They will open ports up upon request, or I could simply extend my web app to port 80 and access it that way. However, links within SharePoint-generated emails from work flows, alerts, etc. point to the initial site's port and URL which, so the latter solution was out. In general using port 80 will be cleaner, but I was concerned about the restore issue.
After a bit of a search, I found no definitive answer. There apparently is a definite problem when you are using Central Admin to restore a backup when there are other web app's on the same port (some people deleted all sites on port 80 to get their restore – ouch), but I did not confirm this as I use stsadm nearly exclusively for restore.
Happily, the title of this post says it all. I created two blank sites on my development machine on port 80 with host headers, backed them both up, made changes to those sites. When I restored, the changes were overwritten.