it is not treated as NoData, but at least phase noise introduces no random patterns inside this area which can distort the result. The latest version of snaphu supports the officially supports masking by low coherence, but this is not implemented in SNAP yet. So you have to run it from the command line and test how well it works. We discussed this here, in case you find a way how to use it and can report: Snaphu unwrapping error - tile issue? - #4 by ABraun
As unwrapping is an iterative process, the results vary between each processing. So even with constant parameters, you might get slight differences. As far as I know snaphu is based on a number of randomly placed starting points and not a single reference point which can be selected by the user. But the snaphu documentation has more information on this.