The GPU acceleration support for Flatpak will be available as recommended packages for Flatpak and will be installed automatically on the next upgrade*. This only covers the FDO 22.08 and 23.08 runtimes which covers the vast majority of Flatpaks on https://flathub.org/. Notability Fedora’s own Flatpaks are unfortunately not covered due to a bug.
* the automatic install requires asahi-repos-1-13 to be already installed (available since 2024-07-15). If this was not the case the runtimes can be manually installed by installing asahi-platform-metapackage-flatpak.