Let us use the Joomla Extension Directory as an Example. It has very customized and perfect categories which some extensions are located in different categories.
Now lets say we have a website just same as the JED, but, the difference is that its not for Joomla only, it has extensions for Joomla, WordPress & Drupal. So, we are going to use the JED categories, and use WordPress, Joomla, Drupal and etc. as tags.
One Extension (or Download) may be in several categories and several tags.
In your particular method, we have to make a download copy for each file in each directory that we want. So, when an extension updates, we have to change the version in each download. if the log changes, or the description changes, we have to change it in every download, and that would be DIFFICULT.
What I am trying to say is that we have to be able to assign a download in several tags and several directories. and if anything changes in the description or other details, we should be able to change it in only one place.
Assigning a download in several categories is very common in WordPress, and it is also easy to do in EDocMan. But JDownload has not prepared such a section or ability.