SNAP Graph Builder save can result in undesired graph changes

Graph Builder prepends undesired absolute local path to file variables, and may append undesired file extension when saving. These lines from the graph before opening, and after saving.
source XML: file>${out}_GEO</file
saved XML: file>/gs/some/contract/2016/TEM/cache/snap-benchmark-tmp/${out}_GEO.hdr</file

Graph Builder can remove variables (from Subset):
source XML: geoRegion>${subset}</geoRegion
saved XML: geoRegion/

Graph Builder fails to open some graphs with variable parameters (from S1TBX Terrain-Correction):