I think, it's better to put MISTer into some retro case like Amiga 1200.
Otherwise you may find some tiny case in radio shack or similar store and make required holes.
Making a breakout board will be too expensive because of size and used male-female connectors. Also size of the whole construction will be huge without any extra added functions.
At least with retro case it will look like retro replica. With this ITX case it will look like face-less brick.
Since MiSTer is DIY project, it's up to user decision which case to use