Ash here from the Shopify team. Welcome to the Shopify Community!
You're correct that Shopify Payments is currently not available in Portugal. This means you will need to select a third-party payment provider which is available in Portugal to process your payments. Here is a list of the major supported payment providers available in Portugal.
As for transaction fees, this does mean that you will be subject to the additional fees when using a payment provider other than Shopify Payments. The transaction fee varies across plans, and the higher the plan tier, the lower the transaction fee. You can see the full breakdown of pricing and features for each plan here.
I hope this helps clear things up, and let me know if you have any further questions I can assist with!