Typically iPhoto (cannot speak for Aperture, but since its the same Library format I guess it is true there as well) "hides" the photos from you "somewhere in the local file system", once imported.
It hides the files and only shows the images instead.
And it places them where it sees fit.
iTunes does as well but still the vast majority has no problem with that.
we all know the original and edited photos are not really "gone", they are still accessible in the "iPhoto Library" which is nothing more than a "Bundle" (or "Package"), so you can still access the files therein (by right-clicking etc.). But the way/structure your photos are stored therein is not meant to be changed (and you better not do it!).
It is not the edited images are gone or not gone, it is simply that with non-destructive editors, the edited photos simply doesn't exist as a file yet until you export it.
This is in stark contrast how e.g. Lightroom organises the photos! The primary structure 1:1 reflects your file hierarchy!
Only in one direction, whatever you move inside LR will be moved in the Finder as well. And the Finder normally only sees the originals, it doesn't see the edited images as they don't exist yet as files. And that is without adding Albums/Collections or Versions/Virtual Copies which also don't exist in the Finder.
In fact, you can mess around in the file system (move/copy/add/delete photos) and then "sync" those changes with the Lightroom hierarchy.
Sure, for the originals you can match inside LR what you do in the Finder manually on a folder by folder basis but that is not automatic.
Off course Lightroom also allows you do organise your photos with "(Smart) Collections" etc., similar to Aperture. But you always have full control about where your photos are stored and how they are organised! (And I prefer that).
As I said, that only applies to originals, not the edited images, not to virtual copies, not to collections and in one direction requires manual action. The advantage is that it lets you more easily use other raw converters and that it reassures people that if LR would fail to launch one day, they'd still see their folder structure.
The disadvantage is that you cannot fully exploit the potential of non-destructive editing as you cannot integrate collections and virtual copies in your normal folder hierarchy but are forced to browse for stuff in two separate folder structures.
But again, this has absolutely nothing to do with the fact that Apple now (re-!)introduced their iCloud Disk (or whatever it is called now).
iCloud Drive just disproves the notion that Apple is so opposed to users managing their own files that would never make it easier to do so.
----------
I'm not really convinced of the comparison there; iPhoto is the basic editor compared to Aperture, but they're now being rolled together into what looks like a photo library manager, with both simple and advanced editing tools.
So the tools in Quicktime Player in that regard are the simple tools, while iMovie's are more advanced (albeit including composition as well, but then Quicktime can copy/paste movie segments too). But my point also is that Quicktime Player lacks the concept of a media library, which means it's in a kind of funny position where for many users it doesn't really do anything anymore, as it's generally better to move your movies into iTunes if you can since it organises them into a media library. But really the opposite would be better; with that media library moving out into its own, movie centric app. Okay, maybe combining iMovie could be a step too far, but I could absolutely see Quicktime Player being replaced with a Movies app aimed at organising your movie and TV show library, with some simple editing tools for tweaking things like home movies.
If you want to view a single movie file, you'll launch Quicktime (or have it launched by just double-clicking the file), this is the same with Preview. And as Quicktime lacks the concept of a media library, so does Preview. And if you want to throw in Aperture, you can compare: Preview -> iPhoto -> Aperture with Quicktime -> iMovie -> FCP.
And yes, you could take out movies and TV shows from iTunes and split the latter into an audio and a video half. But that wouldn't affect QT, you'd still need an app to launch that single movie file you just want to view without adding it to your library, the same way as Preview won't go away because of the new Photos app.