I don't now why you must have all files in the same folder but in different categories. You are the first user in more than ten years with this wish.
But maybe is jDownloads in your case not the right extension for that what you want to do with it.
A modification would be not so easy and not planned by us. Sorry that we cannot help you here. But it exists many other download manager for Joomla.
Another way could be to rethink the structure of the categories and files.
Well, what can I tell you?
Unfortunately these 10 years of experience, you had no chance to meet a case like ours, that's a pity.
My need, as I explained above, in my company we separate the files by category, because it makes more sense for our users, but it can happen that one or the other file is the same for all categories. If all files were in the same directory I could have several downloads pointing to the same file, from several categories, after all it's the same file.
This facilitates from the point of view of the user who will look for files in the category of his area, and allows the company to keep some generic files inside. Still talking about that, in maintenance I would only update one file and not several in several categories.
I may be badly accustomed, because I have used a component for a long time for Joomla that did exactly what I am asking, but now it is paid.
This is it.