Hi Sean,
Thanks for your post. I suspect this is caused by the optical fiber model. I ran some quick test, using waveguides instead of fibers, the results were more what you would expect when changing the length difference. I have to check with my colleagues, it's not clear to me if the group index is defined. Since the FSR of the Mach-Zehnder interferometer directly depends on the group index, it could explain this result.
On a side node, the transmission given by the ONA is the complex transmission. To get the fraction of power, use abs(T)^2.
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