The problem came when I exported the geometry to gdml in /cvmfs/sft.cern.ch/lcg/views/LCG_101 which uses Geant4-10.7.2 with VecGeom probably. The problem seems to be in G4UPara as my local installation (without VecGeom) which uses G4Para works properly. The X size of the G4Para exported to gdml via G4UPara equals to its Z size:
G4double G4UPara::GetXHalfLength() const
It looks like it is also like this in 10.7.3:
If you could confirm that the problem with exporting G4Para to gdml is this one and not something else it would be helpful.