The Portuguese Naming Conventions page actually states that although a person may use all four surnames, it is more common to have one from the mother and then one from the father. The current naming standard was reached after lengthy conversations about the possibilities and difficulties. The 'old' records certainly do present the largest selection of records and therefore there is no surname recorded at birth for the majority of profiles. Rather than put 'unknown' in the Last Name At Birth field, it was decided to put the father's surname that was present on the baptism record. If the mother had a surname, instead of her two given names, you could choose to put that and then the father's surname(s) in the Last Name At Birth field.
For a modern record you would certainly use the surnames listed on that record. In your case it would be [Mother Surname] [Father Surname] [Father Surname] as Last Name At Birth.
As for your question about names in later records, those would not prove Last Name At Birth (it is a literal field - what the name was at time of birth). The Spanish Naming Conventions are not that different. If there is a record that supplies the entire name, you use it. If there is no record of the full surname, you can record either one or two surnames from the father and mother (father's first for Spanish names). Any other combinations go in the 'Other Last Names' field. Most women didn't take their husband's surname, so that is never used unless you find a record proving it.
Here is a 1911 baptism record for Alba, the daughter of Joao Rodrigues Coelho and Vicencia de Jesus. Her First Name At Birth could be 'Rodrigues Coelho' or 'de Jesus Rodrigues Coelho.' As de Jesus is a devotional name I would personally use Rodrigues Coelho, and then use 'de Jesus Rodrigues Coelho' as 'Other Last Names.' You wouldn't mark it as 'certain' but it helps when others are looking at the profile to see the possibilities. Additionally, if it would have been 'da Silva' I would put 'Silva' in Last Name At Birth and 'da Silva' in Other Last Names, as it can create search difficulties on WikiTree and cause duplicate profiles to be created. You wouldn't address someone as Mr da Silva, you would say Mr. Silva, so I am comfortable with that decision.
Going back to the question of assuming a later record matches the Last Name At Birth - that is not always the case. My Madeira ancestors may have been given one surname at birth, and chosen to use others when they came of age. I see more varieties in the surnames as opposed to the Azores ancestors that have kept the same surnames as their siblings. I'm not sure what the difference is on the mainland/Continent. You asked "If it's clear that even after marriage she didn't adopt any of her husband's last name, than why should this be the standard?" But it definitely is not the standard to use a husband's surname for the wife. If this or any of the other sections needs to be made clearer, let me know! We certainly try to make those 'Help' pages actually helpful.
And finally - welcome to WikiTree!! I've enjoyed the conversation and look forward to seeing more Silva contributions to our lovely global tree. If you are interested in joining the Portugal Project you can answer this post. New members are always welcome!