So many flatpaks do this incorrectly though. For Browser by default saves in the flatpaks home/Downloads directory (which is 15 layers deep from ~). You just gotta know to navigate up.
Signal let's you save attachments anywhere on disk, but only if you manually navigate to ~/Downloads, does it actually save (in a way visible and accessible outside of the app). You just gotta know.
I forgot what exactly the problem was with Vscode(/ium), but it also has a catch like that. You just gotta know.
Flatpak turns out to be the best compromise between distribution and cross distro compatibility, but there's still some low hanging fruit that could be improved.