One way to get pricise unwrapping

You can define a valid pixel expression based on coherence. As you said, this is not used when exporting to SNAPHU. But you can generate a new band with the band maths operator using conditions like marpet demonstrated here:

Another way would be clipping by a vector as you suggested:

  1. Digitize a polygon around your area of interest and save your product
  2. Use the Land/Sea mask module to clip out this area: Instead of masking the land or sea, use the third option where your geometry is used as the mask extent.

I am however not sure if this preserves the metadata as required by SNAPHU