Would there be a way to adjust the microlens so that it concentrates just on the photodiode?
I think for this cutout, the microlens is magnified, so the microlens only covers the bottom-right corner with the cutout. That means that the rest of the photodiode likely does not receive light. I wonder if this results in a loss of information or bias, since only part of the photodiode receives light, for all photodiodes.
The usage of microlens can actually increase the effective fill factor up to 100% because it converges light from the whole pixel area onto the diode.
I notice that the design philosophy is really similar to compact light field cameras. There the microlens are designed to divert light rays from different directions whereas here the microlens are used for focusing incoming lights to the diode.