Separate folder-installations not equal to separate configurations?

Ok, in the old days, you could have Atahualpa installed in separate folders (in my case, I had folders named "Atahualpa-jeans", Atahualpa-kitchen", "Atahualpa-books" etc) and customize each one to have a different look. Once you did that, using a plugin like GYS-Themed Categories, you could literally give a different look to your site, based on the category.

For instance, most of my posts had a blue-jean theme, but things under the category "from-the-kitchen" (where I discussed recipes we'd tried) had a different look, while still using Atahualpa as the theme.

Am I to understand that is no longer possible without some serious coding? Is Atahualpa using the same tables, no matter what folder you install it in? Because I just upgraded my main site, and everything matched a previous upgrade made for a new category.