Yes, the pins can be bent by up to about 10 degrees, while still maintaining a good connection. If you need to bend more than that, you should probably consider how the things will connect together prior to assembling the connectors onto the boards.
The program can be altered to do almost anything, although true randomness is hard to achieve on a microcontroller. The Octolively is normally used in a mode where each LED responds to the stimulation at that site, however it does not necessarily need to be built with the sensors, if you do not need them, and your program will not expect them.