I managed to get it working on my Steam Deck with the following steps
but if you are not familiar with the desktop mode and the basics of arch linux it will be a bit hard.

some of the commands used are not available by default on the steam deck.
If you already built an AUR package successfully you can skip these steps.
But keep in mind that some of these steps can become necessary again after a system update.

To get it all working you need to run these commands:

Setup a Password for the deck user with the passwd command:
passwd
disable the read only file system
sudo steamos-readonly disable
Setup pacman-keyring so you can install packages
sudo pacman-keyring --init
sudo pacman-keyring --populate
Install the needed packages for AUR
sudo pacman -S --needed base-devel

Now you can install FAF

Switch to Desktop mode.
Install Supreme Commander Forged Alliance via Steam and go to properties and use the following launch options:

PROTON_NO_ESYNC=1 PROTON_NO_FSYNC=1 PROTON_DUMP_DEBUG_COMMANDS=1 %command%

In compatibility settings select Proton Version 5.0-10.

Then start the Game via steam.
This creates a file called "run" in the location /tmp/proton_deck/run
"deck" is the default name of the user. Change it if your user has a different name.
copy this file to a location where you can find it later. I created a directory called "faf" in my home directory for this and put it there.

then install downlords faf client:
to install it, download the client with git clone

git clone https://aur.archlinux.org/downlords-faf-client.git

then navigate into the downloaded folder with

cd downlords-faf-client

and run

makepkg -si

after this you can search for "faf" in your start menu and launch the program.
Log in with your faf account and go to settings.
Go to "Forged Alliance Forever" and set the start command format to the path to your previously copied run file. So for me it is /home/deck/faf/run
add a space and a "%s" to that path so it looks like this:
/home/deck/faf/run "%s"

Now you should be able to start a Match via FAF.
Some people also changed a specific .dll file in the games bin folder to fix some graphical issues but I did not find a reason for this at least for now.
You can find it inside this tutorial for setting up FAF on linux: https://wiki.faforever.com/en/Linux-Install

@brutus5000
Thats true but you can make a script out of this and be up and running very quickly again.

I created one for me and it works well.

@brutus5000 there is a pkgbuild file inside the AUR repo
https://aur.archlinux.org/downlords-faf-client.git

@brutus5000
Thats true but you can make a script out of this and be up and running very quickly again.

I created one for me and it works well.

I managed to get it working on my Steam Deck with the following steps
but if you are not familiar with the desktop mode and the basics of arch linux it will be a bit hard.

some of the commands used are not available by default on the steam deck.
If you already built an AUR package successfully you can skip these steps.
But keep in mind that some of these steps can become necessary again after a system update.

To get it all working you need to run these commands:

Setup a Password for the deck user with the passwd command:
passwd
disable the read only file system
sudo steamos-readonly disable
Setup pacman-keyring so you can install packages
sudo pacman-keyring --init
sudo pacman-keyring --populate
Install the needed packages for AUR
sudo pacman -S --needed base-devel

Now you can install FAF

Switch to Desktop mode.
Install Supreme Commander Forged Alliance via Steam and go to properties and use the following launch options:

PROTON_NO_ESYNC=1 PROTON_NO_FSYNC=1 PROTON_DUMP_DEBUG_COMMANDS=1 %command%

In compatibility settings select Proton Version 5.0-10.

Then start the Game via steam.
This creates a file called "run" in the location /tmp/proton_deck/run
"deck" is the default name of the user. Change it if your user has a different name.
copy this file to a location where you can find it later. I created a directory called "faf" in my home directory for this and put it there.

then install downlords faf client:
to install it, download the client with git clone

git clone https://aur.archlinux.org/downlords-faf-client.git

then navigate into the downloaded folder with

cd downlords-faf-client

and run

makepkg -si

after this you can search for "faf" in your start menu and launch the program.
Log in with your faf account and go to settings.
Go to "Forged Alliance Forever" and set the start command format to the path to your previously copied run file. So for me it is /home/deck/faf/run
add a space and a "%s" to that path so it looks like this:
/home/deck/faf/run "%s"

Now you should be able to start a Match via FAF.
Some people also changed a specific .dll file in the games bin folder to fix some graphical issues but I did not find a reason for this at least for now.
You can find it inside this tutorial for setting up FAF on linux: https://wiki.faforever.com/en/Linux-Install