I think the method used in Creator is the "last accessed" method, per type. So if I generate a .gcode file in Creator and save it to a folder, it remembers that folder and uses it as the starting place to save the next .gcode file. Similar (but separate) for Factory files, getting STL files, etc., etc. Each type has an associated "last folder" remembered for next time. That's great if you want a folder with all your STLs (where your CAD software saves them, perhaps?) and a folder for all the gcode files (for copying to an SD card, perhaps?), and a folder for FFF files (for when you are calibrating or dinking with settings trying to find the "sweet spot" for that brand of black PLA), and a folder for Factory files (for attaching to a support e-mail when there's an issue, perhaps?).
(BTW, the defaults after a Linux install are in the /opt/S3DCreator area and not in the /home/(user)/Documents space, so the first save/open of each type involves a bunch of clicking..... I'd like to see Creator be more "user-aware" in Linux and start each user's storage somewhere in his/her home/Documents structure.)
But the "last accessed folder" method can be REALLY annoying if you are used to working in a Project folder structure. I think what you (pc) want is to have a Project container with subfolders for all the file types --- one for gcode, etc. --- and have the ability to open a "project" by name to get to all the associated stuff. (A project, of course, could consist of multiple "parts" --- with STL, gcode, etc. for each.) Say I'm working on "StatueOfWife", and within that project perhaps I have places for gcode, STL, fff, factory, etc. --- or just all in one folder even, for a small project. I finish my progress on that project and close it, then open the "ToyForDog" project and work on that, with all the files for that project structured the similarly, but only for that project.
At least that's the sort of direction I THINK you'd like to see it go, right?
I think there are benefits for each. The former (S3DC default) works well if your workflow involves getting something from Thingiverse, loading it, applying your standard process, slicing, saving gcode to SDCard and printing from SD card. (The saved STL location could be the output folder of your CAD package, and the gcode location could be the SDCard mapped drive letter...) The latter works better if you have multiple projects active at a time for multiple customers and need to work on one, then put it to bed and work on another.
I think Creator uses the former layout to make it easy for new users to get up and running slicing and printing objects found on the Internet. I agree it would be nice to have a selection for which way to structure files, "NewUser" (remember folder for each file type) or "MultiProject" (use a standard structure and offer to open and close "projects"). I can live with the method used because I'm new at this and not developing multiple objects for multiple customers under project deadlines --- I'm just a hobbyist building enclosures for microcontroller projects and other "nifty" stuff, like presents for family. But I can foresee a need to have multiple "projects" in the future so I can better keep track of all the neat stuff I want to make.
I guess it's just up to Clayton et al to decide whether they want to keep the current file structure or add a "project" structure option. Some software vendors do this by providing a pricier "professional" edition..... So I guess the real question is: How much are you willing to pony up for this feature?