Photo organizing software is generally of two types, browsers and DAM/PIEs.
A browser just browses folders that have images in them. Maybe showing just the images, or allowing albums to be made that are really links or paths to the photos. The images themselves are kept in what filesystem arrangement the user wants. Lyn, AfterShot Pro (in part), Graphic Converter, on the Mac do this.
DAM/PIE's are digital asset managers, usually referring to an application that stores info about the images (metadata), location of images, adjustments to images, etc in a database. PIE's are parametric image editors, which means in addition to organizing photos, they can store the adjustments to those images in the form of data in a data, so the image itself doesn't have to change: you're storing the info about those changes, like storing plans for a remodel rather than the remodel building.
Both have advantages. The browsers can be fast; the info about AfterShot Pro is a bit vague because it can operate like a browser and show pictures quickly; Lightroom by comparison will import images and create it's own previews and copy them to whatever locations you choose, etc. The PIE's can store a ton of info about one image, like several versions in BW, sepia, different crops, etc, all without having to output a file, like one does with "save as..." in most operating systems. Saves space, and speeds things up.
DAMs can work in two ways, either by managing image files, or referencing them. In managing, the application (like Aperture) copies the image off the SD card and puts it in it's own filesystem, or library in the case of Aperture. It's a date-based scheme that is hidden from the user in a special folder called a package.
Others, like Lightroom, only reference images; the images are put where the user put them in the filesystem (say a Pictures folder), or where you instruct Lr to copy them. But they are right out there like any Word, text or other user data file, not hidden in a library. The locations (paths) are stored in Lr's catalog, NOT the images. By default it will copy off an SD card to a date-based file structure in the Finder, but there are lots of ways to customize that.
Unfortunately you seem to have missed the fact that Aperture can EITHER reference OR manage photo files. You can instruct it (or iPhoto or Photos) to not copy the photos into its library, and instead reference them. So you could put them in any old file structure you want, and if imported from there, Aperture will treat them as it would photos copied into its own library.