[VnV][telemac3d] Update gouttedo/thompson examples with better choices

- TREATMENT OF NEGATIVE DEPTHS = 2 (new default value since release 9.0) and
TIDAL FLATS = YES (default value) to improve mass conservation of water
for both examples gouttedo + thompson
- FREE SURFACE GRADIENT COMPATIBILITY : 0.8 for thompson example to decrease
spurious oscillations: 0.9 is not enough, 0.8 is OK, 0. is not so needed