TLDR;
Install plugins to
/var/lib/flatpak/app/org.ardour.Ardour/x86_64/stable/active/files/extensions/Plugins/
(note that your architecture folder may be different, check your filesystem to find the exact path)
Working in this directory will require
sudoprivileges.
VST2 plugins go in a subfolder named vst and VST3 plugins go in a subfolder vst3. These subfolders probably need to be created.
In the plugin preferences I could see that the VST2 path is /app/extensions/Plugins/vst and the VST3 path is /app/extensions/Plugins/vst3. I just had to find where that was located within the Ardour flatpak installation.
Potential issue: flatpak may create a new folder structure when Ardour is upgraded. You may have to reinstall the plugins after Ardour upgrades.
What did NOT work: using flatpak override to provide access to the “standard” VST3 locations. I tried $HOME/.vst3 and /usr/local/lib/vst3. IMO this would have been a cleaner solution. Does Ardour look in these standard locations when running as flatpak?
The Ardour UI discourages modifications to the VST3 path (for reasons not explained), so I didn’t pursue that option. Maybe I could have used a different location and provided access via flatpak override.