I'm thinking that I would be #2 which would require permission to enter Portugal
Keep in mind that these rules are intended to apply to all passengers, including those that require specific visas to enter a country.
In your case, carrying a US Passport, that is your "permission" in that US Passport holders are entitled to visa free travel to a Schengen country for 90 days out of 180 without (for now) further permission. Of course, entry to any country is at the discretion of the border agents.
In regards to what constitutes "vaccinated"; some countries are setting limits on validity after the last shot or booster, but the Schengen countries are trying to align their requirements, so probably, what goes for Portugal, will eventually go for the Netherlands. The UK of course is completely separate.
However, I would not be concerned about getting stopped in the Netherlands due to vaccination issues while in transit, the airline will not let you board unless you meet requirements. So look at meeting Portugal's requirements, plus any transit requirements for paperwork to get through Amsterdam, and you will be fine. For better or worse, once the airline clears you for travel, no one will look at vaccination status.
This is for entry only though, once in Portugal, or the UK, separate requirements may be in force for entering a restaurant, a museum, or other venues.