I've tried both the vanilla GNOME session and the Ubuntu session, I've tried using the toggle or the command line ('gsettings set org.gnome.desktop.interface color-scheme prefer-dark'), I've tried .deb apps and Flatpak ones and while all apps respect the light/dark setting, bringing up the file picker in any of them will bring up a light mode version of it even when using dark mode.
Is everyone having the same problem? And if so, have you found a solution?
Edit: Upon further experimentation, some of what I said above seems to not be accurate. For one, some .deb programs will indeed call the dark mode file picker (for example, gnome-text-editor), but they have to be programs that use libadwaita to call on the new file picker, ie. the one that has a thumbnail view. So gnome-text-editor will call the new one, while gedit will call the old one.
But other .debs (notably Chrome) as well as all Flatpaks and Snaps (including libadwaita apps and the Firefox Snap) will call the light mode file picker no matter what. So what I assume is happening is probably a bug with xdg-desktop-portal not being able to detect the light/dark mode preference. I'll keep digging but this lowers my hopes of finding a fix fox this...
Edit 2: I have found this bug which matches the issue. Hopefully it gets activity, so at least it will be useful for tracking. Haven't found a corresponding bug upstream, so I'm now making a VM to see if I can reproduce the issue on other distros using GNOME 44.
Edit 3: Testing on a Fedora Silverblue 38 VM, the issue was not reproducible, so this does seem like an Ubuntu issue.