How to migrate Host Named Site Collections from SPS2003 (4311890)

I am migrating from SharePoint Portal Server (SPS) 2003 to SharePoint 2007 (or 2010/2013) and the SPS 2003 farm has several host-named site collections. I don't see a way to migrate those site collections using Content Matrix.

The source is not using Host Named Site Collections, they are SharePoint 2003 bucket webs. They are automatically created by SharePoint and were deprecated in 2007.

Instead of trying to preserve the paths containing "C0, C1, C2, etc.", migrate the entire root site collection or break it up into multiple site collections on the target.