On scanning the reference document about the effect of pulsed light on vegetable growth, I began to wonder whether the authors really controlled their experiments appropriately to justify their interpretations. I did not see anything that suggested they did a spectral analysis of the led output at each pulse frequency to ensure that no wavelength shifts where occurring. A quick (maybe too quick) search suggested that there can be circuit temperature effects on the led wavelengths. Whether that could lead to spectral shifts large enough to affect growth, I do not know.
I wonder if there are good references describing intensity-pulsing-wavelength shifts in leds that might be appropriate, and might influence the direction of your study, as another degree of freedom.