currently not possible to configure an exe with custom arguments, i'll consider adding it in the C rewrite if it isnt too complex to fit into the db migration schema.
what you can do currently is configure URLs, this for example works with steam games that have a uri for the steam client. if there is one for lutris, or youre willing to set up a custom one that transforms a uri path into an argument for the command you want (linux makes this fairly easy), that should work in the meantime and maybe even easier than setting up a command with multiple arguments for each game, you could have custom-lutris://game-id and the script bound to handle that uri protocol converts it into flatpak run net.lutris.Lutris lutris:rungame/game-id. though the syntax of that lutris command makes it look like lutris already has a uri handler, might just need to configure it to be available for the whole system rather than just the flatpak sandbox, if it isnt already.