I definitely agree that the Bom Jesus do Monte near Braga is one of Portugal's remaining premier sites. (I have a soft spot for the country, as my wife and I went there for our honeymoon and were enchanted. It was also my introduction to Iberia). I am actually really surprised it took them this long to nominate it. I think Mafra is splendid, and there are certainly Baroque churches in Porto & Evora, as well as areas of Lisbon if that city, even just the Baixa, were to be inscribed (which it should be).
However, the Bom Jesus is, as you say, peak Baroque. It is a masterpiece. I would agree that it fulfills category i, as well as ii, as we can see this type of architecture in colonial Brazil and other parts of Iberia. I know that Congonhas has already been inscribed, but if it was up to me, this would have been inscribed first, as it was the progenitor and is much more architecturally, aesthetically, and culturally important. It also, to some extent, represents aspects of the "Portuguese Plain Style" of architecture, discussed by George Kubler in his book dedicated to that form. Kubler is the author the extremely important "The Shape of Time."