It works partially with Flatpaks on XFCE (or any desktop)
It can change the icon for the Flatpak launcher that appears in your menu. It edits the user .desktop file that Flatpak generates (usually in ~/.local/share/applications/).
However, Flatpaks are sandboxed, so changing the icon inside the Flatpak itself (what you see when the app is running) is not possible with this tool — that would require modifying the Flatpak bundle.
So: menu/panel icon = yes. In-app icon = no.