Yes, a conventional 2-port MMI will generally give you a pi/2 phase shift of one port relative to another. If you combine the 2 ports again with another MMI, you have built a Mach-Zehnder interferometer with ideally pi phase difference (if you've perfectly matched the length of the 2 waveguides) between the top and bottom signal paths. If you insert a phase shifter in one or both arms you can control the light at the output of the MZ by varying the voltage applied to the phase shifter. You can then modulate the voltage and produce an AM or PM signal at the output of the MZM. This is currently how some commercially available photonic communication IC's send data over the network.There are limitations on how good the extinction (cancellation) can be based on how well the losses are matched in the respective waveguides.
In this case of this paper, I imagine that the phase relationship will be much more complex and it will highly wavelength dependent.
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