The AdditionalEosUpdater variable is an advanced feature. It may contain the name of your external script. The script is meant for performing other tasks related to updating your software. It is called right after updating Arch, EndeavourOS, and possibly AUR packages. One useful example of this is to have a script that updates your flatpacks. The script gets the name of a log file as a parameter and can add log information if needed. The script should provide an exit code similar to the checkupdates program (0, 1 or 2).
if I understand the part correctly you would have to write a script for it?
This is a more or less experimental feature in eos-update-notifier, but it should basically work if you add a proper command to the variable.
The command can be e.g. a script, or e.g. a program written in C language.
So you are fully in charge of what the command does, and eos-update-notifier is simply able to call it, and use its return code as explained.
I’m not using flatpak so don’t know about that.
In principal you could do the update anyway, but the only small issue is the return value.
Can you parse the flatpak command output to see if there were updates? Then you would know what value to return.