It is possible to create custom sketches to use with Breakout. See the readme file in Breakout/custom_examples/ and the rfid_example2.html file in the same directory.

There is also work in progress on a one-wire firmata sketch. See the thread here on the Breakout github page: http://github.com/firmata/arduino/issues/10

Also see this post on the firmata dev list: http://sourceforge.net/mailarchive/message.php?msg_id=30238158. It describes how to create a sketch to communicate with Breakout.

Keep in mind that by using a custom sketch you will not be able to use the Breakout IO objects (unless you specifically implement support for them in your sketch… which is difficult), you will only be able to send and receive sysex and string messages.