[VnV][telemac3d] Update stratification example with better choices of keywords

- TREATMENT OF NEGATIVE DEPTHS = 2 (new default value since release 9.0)
to improve mass conservation of water + tracer
- use of gradient conjugate + preconditioning 34 = 2*17 to solve PPE, quite
more efficient than GMRES for this example
- switch to non-hydrostatic version (default) but no significant differences