The upside of having the system draw file dialogs is that file dialogs from different apps look consistent, rather than getting out-of-place dialogs depending on what toolkit the app used. It might sound silly, but it's a real annoyance, and there are plenty of apps that don't implement any custom preview.
Oh sure, but it's hard to make a one-size-fits-all file chooser. The case in point: Gimp, not using GtkFileChooserNative, even though Gtk started off as the "Gimp ToolKit". Otherwise, Gimp does not get image previews.
Even if you do build support for previews in the file chooser, you lose the sandboxing since that preview-generating app now has access to any file a user simply previews. Unless you start introducing a separate, orthogonal previewing system, you also lose caching of generated thumbnails and such.
But it's not only previews: there's also the File-Roller (archive manager for GNOME) "Add File" file picker.
So, while it would be great to have consistent file choosers UX- and UI-wise, you'd be forcing some apps to do away with useful features. And suddenly, you are now into how much consistency matters in this particular case?
FWIW, some issues will remain forever (or well, a long time): in the days of gnome-vfs vs pure Gtk+ file choosers, one could give you non-local files [nfs, smb, sftp...], and the other couldn't, yet they looked exactly the same.
The same is true for Gtk file chooser today (local vs networked files), simply because some apps can handle them, and some can't. These UX issues always annoyed me more than the look of file choosers between apps.
In a sense, I am actually arguing for orthogonal, system-wide file chooser infrastructure with support for everything and your kitchen sink. These would now not be sand-boxed (I don't want to wait an hour for my gallery image previews to load, so caching FTW), so it's a big attack surface (all the previewers, with some like ghostview executing turing-complete PS programs), and it makes you question why would you need sandboxing for the rest of the stuff :)
Thumbnail rendering on GNOME is already sandboxed with bubblewrap, even when you're outside Flatpak: [0] for docs and [1] for code on how they accomplish it.
I don't think it's possible yet to ship thumbnailers in Flatpak - I'll try poking someone to see if there are plans for that.
