I can see how that might be expected, but that would be messing with the default URL rewrites in WordPress. I felt (and continue to feel) that while adding the built in taxonomies is a nice thing to have for many, changing how the URL scheme works is outside of the intended scope of the plugin.
For users installing it on an existing site it would mess with all the current links (by moving pages in to the /%category%/ structure). So really I'd need to provide some toggle but I know that most of the users of the plugin would not realize the consequences of the switch and support would increase.
The short version is, valid question. No plans to include that as a base functionality. I'd suggest hiring a developer to add that to your site. I get Brady at BlazerSix to do that type of stuff since I find Regex a pain.