The DAW (Pro Tools in this case) has no knowledge of what is connected to an ADAT input. All it can know is whether there is a clock arriving there, and offer you the option of using that clock as your sync source.
You could try the experiment of connecting the Apogee's ADAT output round to its ADAT input to see what happens in the control panel. The clock phasing is guaranteed in this case unless you select ADAT as the source, when it all goes haywire.


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