Okay, found it:

flatout.exe -setup

(Wasn't easy for me to find out as I run Linux.)

Sweet, you found it? where is it? i also use linux, and cannot find that file anywhere. ive installed flatout using playonlinux, if that is any help

Isn't there a config.exe or something? It's weird that you would have to run flatout.exe -setup.

unfortunatly, this game doesnt have a config file.. the configuration for the games graphics come up when you run the executable. now, when using wine, it launches the game directly, without using the executable, thus why it doesnt pop up. the relic of an older age.....

What does this even mean? Computers only execute executables. Wine executed windows executables, but it is the same concept.

I am having the same issue - Linux Mint 17 - I got a new monitor and the game is playing on the old resolution.

In case this is still relevant to anyone in the future, you can open the start.sh file in your FlatOut 2 folder and edit it with a text editor.

Edit the function run_game() {...} like this:

run_game() {
echo "Running ${GAME_NAME}"
local EXE_PATH="drive_c/GOG Games/FlatOut 2/"
local EXE_NAME="FlatOut2.exe"
local EXE_ARGS="-setup"
run_wine "${EXE_PATH}" "${EXE_NAME}" "${EXE_ARGS}"
}

run the start.sh and the dialogue should appear. Once your done reopen the start.sh file in an editor and revert the
function run_game() {...} back to this:

run_game() {
echo "Running ${GAME_NAME}"
local EXE_PATH="drive_c/GOG Games/FlatOut 2/"
local EXE_NAME="FlatOut2.exe"
run_wine "${EXE_PATH}" "${EXE_NAME}"
}

Done. Run the start.sh and you should get the normal game to launch.
note: this is only intended for Linux users, if you run windowed you will have to edit the run_windowed() {..} funktion instead [adding the local EXE_ARGS="-setup" and the "${EXE_ARGS}" ]