Add additional non-rewrite .htaccess directives on multisites via mod_rewrite_rules filter
There is no built-in way to do it. The .htaccess is “printed in the screen” of the wp-admin ones you are setting up the multisite (the same for wp-config.php). That info is never write directly in .htaccess file like the single site. The wordpress core code for multisite / htaccess is here: https://github.com/WordPress/WordPress/blob/703d5bdc8deb17781e9c6d8f0dd7e2c6b6353885/wp-admin/includes/network.php#L543