Hej,
the bootloader is activated when the chip restarts, the button on board happens to be the reset pin, it plugs the Atmega off for as long as the button is pressed. So the actual way the bootloader works is to get active on reset or when plugging the board to power/USB.
The code is opensource, meaning you could rewrite your own bootloader based on our code. Our version is a modified one from a previous program by a different designer and we are keeping his very same license.
On the other hand, you could of course modify the bootlader to be getting active when there is a certain sequence on the serial port (e.g.) but this would force you to use interrupts.
Hasta pronto,
/David