AVR's output, even in the push-pull mode, isn't a strong voltage source in that it has substantial output resistance. So even if you short the output pin (in a logic 1), you don't get much current (40-50ma maybe) out of it. The design here isn't a great design but it is not a deadly design either.
One of the schematics linked here had the led between Vcc and the transistor, without a resistor. If that's really the design, the led can draw substantial current under a 5v rail. Leds are pretty good at taking abuses but it is wise to put a resistor in serial with the led.
But that is just my guess.
It could have been designed for an open - collector type of output pin.