Not sure if it was directly stated in the master's thesis above but if you hook up TTL to an anolog input that expects 0 to 5v you might not be fully turning the laser on and off since the low TTL may be slightly > than 0V and the high TTL may be less than 5V.
I have an analog diode driver but I can adjust the low and high so I can adjust it to give me the proper outputs regardless of it I hook it up to TTL or analog outputs.