For Quad, the node ordering is
Quadrangle:
v
^

32
  
  
 +  > u
 
 
01
Thus the geometry of the plane surface should be follow the above ordering. Otherwise, the calculation of cell Jacobian would be negative. In NFS, the node ordering is converted to the natural IJK ordering. Thus It should have no effects.
I encountered this problem and open an issue in the Gmsh repo. Later on, the developer replied but I did not try to figure it out. Check this link.