If I were starting a company in Portugal tomorrow, here is what I would do.
I would get my NIF before anything else. Nothing moves without it, and as a non-resident it takes longer than people expect.
I would not touch the "incorporate in one day" online packages until I knew the answer to one question: who will this company pay, and how?
Salary and dividends are taxed differently, and the structure you pick on day one decides how expensive it is to take money out later.
I would open the bank account before I needed it. Portuguese banks ask where your money comes from, and they ask properly. Having source of funds documents ready turns weeks of waiting into days.
I would keep the structure boring. One company, simple ownership, no holding structure unless there is an actual reason for one.
Complexity costs money every single year, and most small companies never needed it.
And I would spend one hour with an accountant before registering anything. Not after. The most expensive mistakes I see are all decisions that were locked in at incorporation and discovered at tax time.
None of this is complicated. It is just the order almost nobody follows.