This might be a more theoretical question. As you mentioned, with the phase shifter, the transmission is good. This might be the reason people use it.
When light is not well confined inside the waveguide, scattering causes losses. Thus the longer the device the smaller the transmission. You can verify this by using top and bottom as well as side monitors.
You may also try EME in MODE, as it is more efficient for long repeated structures. Please refer to this example:
https://optics.ansys.com/hc/en-us/articles/360042304334-Bragg-Grating-full-device-simulation-with-EME
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