What happens if Rafael marries unequally but decides not to renounce? Is unequal marriage an automatic disqualification even if he marries with his parents blessing to a Miss Smith?
In the event that he marry unequally and not renounce (very unlikely, from all I know about H.R.H.), there's really no problem.
There's no mention of Dynastic Marriages in the Imperial Constitution, from 1824, that was a House Rule introduced by Princess Isabel (1846-1921), the Head of the Imperial House, 1908, when her oldest son, Prince Pedro de Alcântara (1875-1940), decided to marry an Austrian Countess.
The Imperial Family is tied to both the Imperial Constitution and the House Rules, but only the first have a real legal authority. Prince Rafael isn't required to marry equally, nor to asks the Head of the Imperial House for consent. The only one who can take away his succession rights is himself, signing a renunciation document, like his uncles and aunts.
There's even an precedent for an unequall marriage been considered Dynastic by the Head of the Imperial House. In 1948, when Princess Pia Maria (1913-2000) married Count René of Nicolay (1909-1954), her brother, Prince Pedro Henrique (1909-1981), accepted their union as a Dynastic one, and Princess Pia Maria kept her rights to the Throne. Her sons aren't Brazilian Dynasts because they were registred as French citizens.
So, Prince Rafael can marry anyone, if the girl are going to be a commoner, Prince Luiz will not be very happy, nor will Prince Bertrand, but they can do nothing.
But I have to say, if Prince Rafael decide to marry unequally, he will renounce his succession rights, unless the Head of the Imperial House say that the marriage will be considered as Dynastic. The members of the Imperial Family has a very strong sense of duty regarding the House Rules.