No Both drawings are accurate, one (the first one) is a 5V bus adaption and the second one is a 3V3 buss. To use it on a 5V bus add the resistors from the first drawing or some just like them. Neither is wrong, just for different bus voltages and the first one shows how to convert the second.
I don't follow you. What do you mean as 3v3 buss? The supply coming from the USB connector is 5v. The voltage is going to the ATMega chip. It is going to output digital logic levels of 0v and 5v. In the second drawing, when it tries to output a 5v signal, the zener is going to drag it down to 3v3 without the benefit of a current limiting resistor. Also the output signal going to the USB data lines will be diminished by the inline resistors. If we assume that the normal USB data line is a high impedance input then maybe the resistors (62 ohms) will have little effect.
Is it clear why I am confuses?
Can I conceive of a reason the the second circuit could be correct?
If the input 5v were reduced somewhere to 3v3 before powering the ATMega. This didn't happen
If the USB data lines were driven at voltages above 3v3. I don't know that they are. I am no expert on the USB standard.
If you wanted to protect you ATMega from the high voltage USB data, then maybe the second circuit could be correct.
Basically it does not adhere to the design of Thomas Fischl.