This is not exactly correct. You can annex a country if the total peace cost of all of their provinces is less than 100%. In Europe, this usually means countries with up to 3-5 provinces, more if the provinces are poor. The only influence CBs have on this is that they might reduce the peace cost, making you able to annex larger countries. And of course they can reduce the infamy of taking those provinces, because taking provinces for 4 infamy each means that you can maybe take 1 province every 4 years or so, probably less in the beginning.
As for capitals, you can't demand those in peace deals (except for annexation, of course) unless they are isolated, meaning that the country has not adjacent provinces, and if the capitol has a port, also no other coastal provinces.
For the shamanistic and animistic countries, which apparently are considered heathen primitives, and for colonies which are not yet self-sustaining, you also gain the possibility to simply take their land without a peace deal, and usually for a pretty small amount of infamy, too. However, both of those are different situation than simply wanting to annex some country. And in that case, the tooltip states the problem: "The total peace costs of their provinces are too high", or something along those lines. Portugal is to large to be annexed in one war unless you get a good CB, that is correct.
