The reason for this is that I want somewhat categorized permalinks. Let's say I file a bug and I want the permalink to be /css/ie-bug/ while being tagged as floats, double-margin, margin.
Would it go against the whole purpose of having tags by not tagging this as css but instead categorizing the entry? I would also not tag this as internet-explorer but instead categorize it as well.
Personally, I'd do it the same way. Permalinks (or permalink prefixes) and tags are not the same thing. Tags is very dynamic metadata that gives you the most important properties of your questions. Permalinks are (of course) static and very permanent data that shouldn't be more as a link. So using this logic it's very normal to use a different extra datamodel for permalinks, even if it introduces categories next to tags.
Just my two cents of course.