If your theory were correct, there would then be two possibilities. The first is that this mechanism is "blind", in that it produces hydrocarbons regardless of context. The second is that this mechanism is "smart", in that it produces hydrocarbons dependent on the orientation of the light source. If I had to choose one, I would probably choose the first simply because the algae would generally not need, therefore not develop a "smart" system, since the sun is always "up". However, I can think of few examples where the smart system might be beneficial.
That said, if we assume the first, light placement shouldn't matter, all else being equal. However, over time in an artificial environment, it is feasible that the algae may develop a "smart" system, where it was not before, as it is forced to adapt to this new envirnment.
It would be a good experiment to perform with light source at the top as the control and the light source at the bottom as the experimental. Measure lipids, etc.