From the study you linked it seems the pulsed light has quite minor effect on the growth of the flowers. You are still worried about this effect. Did you consider the light intensity from LEDs does not change linearly with current? To get precise light intensity you need some feedback. And LED light is not homogenous in all directions - maybe you should measure intensity in more than one point. And each LED has slightly different characteristics.
Maybe it is no problem but I think it may be easier and more reproducible to use high frequency PWM and change the duty instead of trying to change the light output by controlling current.