Actually... not so fast.
The title screen indicates that this is version 0.1.1, not 0.1.3 (what happened?), and the ability to remap buttons appears to work at first glance, but no remapping ever becomes active.
Try it for yourself: Go to Options, Joystick Action Setup, and change the two actions (Jump and Run) to B and X instead of A and B. Then, in-game, hold X and press B to jump. Tux doesn't jump. The mapping is still A and B.