For reference, you may want to read the update_option documentation. The arguments you are passing are completely unrelated. However, your third technique is the closest, you have to update all the options in the the update_option call, not just the one option you want. This is because of how the plugin is storing it’s options as an array rather than individual options.
update_option takes two arguments, the first is the name of the option you want to update (in this case se_options) as a string, the second is the option value, this can be almost anything, it will be converted into a string (serialized) by WP when stored. The Search Everything plugin is sending an array which holds all of it’s option settings, you need to do the same.
function nebula_plugin_force_settings() {
$se_options = get_option( 'se_options' );
$se_options['se_use_highlight'] = false;
update_option( 'se_options', $se_options );
}