Does a Buck-Boost Converter/PWM controller significantly reduce the energy you can get from solar panels?
if I have PWM technology or a buck-boost converter that deems I need a
  duty cycle of 0.4 to reach the voltage I want... does that mean I
  don't generate power with my solar panels 60% of the time?


Not if the converter is properly designed. You are probably thinking of a buck circuit that looks like this:-







simulate this circuit &ndash; Schematic created using CircuitLab

If it was this crude then you would be correct to assert that the solar energy would not be fully utilized, because current would only be drawn from the panel during the 40% PWM on-time. 

I simulated this circuit in LTspice and graphed the current through M1 (which is essentially the same as the solar panel's output current):-



When the FET is turned on it draws up to 1A from the panel, but when off it draws nothing! 60% of the time the panel absorbs the solar current internally, wasting it. As a result the power output is only 1.7W, nowhere near the expected 5W.      

But there is something missing from this circuit that all properly designed converters have - a reservoir capacitor across the input. After adding a 220uF capacitor across the panel, and lowering RL to 0.85&ohm; to maintain 2.0V output, the current through M1 looked like this:-

   

The reservoir capacitor eliminates the 1A current limit, so the converter is now able to draw up to 2.6A (1A from the panel plus 1.6A from the capacitor) producing 4.8W at the output - 96% of the panel's capacity. During the 60% PWM off-time the solar panel recharges the reservoir capacitor at 1A, so it is always working at full capacity.