If you need to set different currencies for the minimum order amounts for free shipping and costs for the flat rate, enable the option Enable multi-currency shipping options available in the General settings.
Now go to WooCommerce> Settings > Shipping and select the shipping method to configure the different costs based on the currencies enabled on your site.
Flat rate example
Free shipping example
Please note: if the general option is disabled or if one or more currency fields in Free shipping and/or Flat rate options are left empty, the plugin will convert the costs based on the currency selected by the user.