Since both "references" we are handling right now are The Binding of Isaac and the original Zelda, I would recommend looking at both games again. Probably from what you remember, the images _should_ be drawn at an angle, however if you look at them again you will see that the characters are drawn almost as if seen straight on, and then placed on a "fake" perspective room, which once looked at in static images look "wrong" in a perspective (they however work perfectly well within their context).
In _this_ manner of drawing, the height of the rectangle would be the height of the character. Making a realistic height of a character while moving inside a proper 3d (or fake 2.5d) room would require a lot more math than Casey will probably use in this project (and would change the project into more of a 3D project).
My initial intention with this post was merely to say that when a character is a cartoony character(as the hero's rendering in this very page suggests will be), its height will be much more related to heights of both the background and other characters/items in the world. Its width, on the other hand, has more to do with the artistic style or the character's aspect than any real measurements would have.