Here is a video of a 1 second square wave pulse through the transistor in the shunt configuration.
For the next two traces, I am using an identical LED as the sensor. The square wave signal is around 90hZ.
Here is an oscilloscope trace of the series configuration
And here is a trace of the shunt configuration
With this arrangement, it doesn’t appear to make much of a difference which one you use. The only thing is that in the shunt configuration, the control signal determines the off-time of the transistor, while in the series configuration the signal determines the on-time of the transistor. This may be an effect of using an LED as a detector rather than a more dedicated device like a photodiode or phototransistor.