The main Chrome flatpak currently just installs the official RPM file for Chrome. You're right that the Chromium and Ungoogled Chromium ones do seem to build from source a bit more. I imagine it will just mean a better build process with less patching.
But you can see exactly what it means right in the ticket:
- Create chrome/installer/linux/flatpak/ with packaging scripts and
templates for metadata, AppStream metainfo, and launcher entrypoint.
- Add enable_flatpak GN build argument (default false).
- Add package_format to InstallerConfig and omit host desktop integration
artifacts (system desktop files, /usr/bin symlinks, AppStream appdata,
GNOME default apps, manpages, and AppArmor profiles) when packaging
for Flatpak.
- Update common/installer.py with Flatpak configuration and App ID
mapping for Chromium (org.chromium.Chromium*) and Google Chrome
(com.google.Chrome*).
- Generalize common/desktop.template to support both Flatpak and
system-wide desktop execution commands.
- Disable setuid sandbox and zlib compression for non-official builds.
- Update BUILD.gn with flatpak packaging targets and aliases.