I think whether the style of the portrait matches the sprite, is completely subjective. The in-game graphics are not 100 percent realistic, they are a representation of the characters that has been exaggerated to accomodate the gameplay. You could make a game like this with extremely realistic-looking characters but you would lose a lot of the readability since the details would have to be so incredibly small. So there is a clear advantage to making short stubby cute characters for the onscreen battle stuff.
With the portraits there is no such handicap; with the size they are, an artist is freed up to do whatever he wants. With all of that detail to work with, it enables the possibility of showing subtle nuances of the character; I would argue that this is the entire point of the portraits - to give us a much better idea of the character's appearance, personality, etc. So the advantages of making everyone look like cute anime clones suddenly vanishes. (A good example is Final Fantasy Tactics, a game that I love, but the portraits are worthless. Everyone looks exactly the same, even the exact same facial expression, so why bother?)
Short version: The characters on the map are more like icons of the characters. They represent only the basic facts like what kind of armor they're wearing, and some small details like hairstyle. The portraits because they are much larger can fill in details like age, personality, history, emotion, origin, pedigree, and the list goes on and on. This should be taken full advantage of IMO. They should be drawn in whatever style is best/most comfortable for making a detailed description of who that character is.