We found that applying the subset operation sometimes produces results that don’t perfectly align with the full image. As someone pointed out, "The subset has an upper left coordinate that is exactly a multiple of 10 meters from the original image, however, the subselect region is some arbitrary rectangular area (i.e. not aligned with the pixel grid). Somehow, the SNAP subset step resamples to the nearest whole pixel, which causes the difference. "
See attached XML file that reproduces the problem (change the path from /data/s1 to wherever S1A_IW_GRDH_1SDV_20200427T092438_20200427T092503_032311_03BD30_2747.zip is saved)