You could indeed use a level shifter between the 3.3V and the 5V. So that you can play safely with the 5v without damaging the Rpi. You could use something like this and you could also made it by yourself. If you use it without the level shifter it is possible. As long as you connect the pullup resistors to the 3,3v rail and not to the 5v rail. And the atmega will not set his output to high. Then the 5v is going to the rpi.
Did you study my comments about the zener diode, and how to use them? And why in your case the zener diode will not give you the correct voltage that you want. (tip: it is in serie (draw it on paper and see the result), when the output of the NE555 is "loaded" the voltage will drop (Figure 4).