How to avoid creating first submenu page that is same as menu page?

You can set slug of a subpage to be the same as slug of parent page. For example:

public function onixion_admin_menu_option() {
    add_menu_page('onixion',
        'Onixion',
        'manage_options',
        'onixion-admin-menu',
        array(&$this, 'onixion_main_page' ),
        'dashicons-chart-area',
        '200'
    );
    add_submenu_page(
        'onixion-admin-menu', 
        'scripts',
        'Scripts', 
        'manage_options',
        'onixion-admin-menu',  // <-- here we set the same slug as for parent page
        array(&$this, 'onixion_scripts_page' ) 
    );
    add_submenu_page(
        'onixion-admin-menu', 
        'custom_footer',
        'Custom Footer', 
        'manage_options',
        'custom_footer',
        array(&$this, 'onixion_custom_footer_page' ) 
    );
    add_submenu_page(
        'onixion-admin-menu', 
        'file_upload',
        'File Upload', 
        'manage_options',
        'file_upload',
        array(&$this, 'onixion_file_upload_page' ) 
    );
    add_submenu_page(
        'onixion-admin-menu', 
        'payments',
        'Payments', 
        'manage_options',
        'payments',
        array(&$this, 'onixion_payments_page' ) 
    );
}