Next time please post in the proper forum in order to get quick reply.
A1: Since 2D is a simplified method and the actual device is 3D
A2: You can optimize it but from my experience. limited to process techniques, people have fixed depth parameters.
A3: In optimization the algorithm will pick up a set of parameters to be optimized for each generation. So they are optimized all tegother. Please refer https://optics.ansys.com/hc/en-us/articles/360034922953-Optimization-utility
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