[VnV][telemac3d] Update bottom_bc example with better choices for a few keywords

- TREATMENT OF NEGATIVE DEPTHS = 2 (new default value since release 9.0) and
TIDAL FLATS = YES (default value) to improve mass conservation of water
- use of gradient conjugate + preconditioning 34 = 2*17 to solve PPE, more
efficient than GMRES for this example (very few iterations are needed)
- ACCURACY FOR DIFFUSION OF VELOCITIES = 1.E-15 as easily solved
+ PRECONDITIONING FOR DIFFUSION OF VELOCITIES = 34 to improve efficiency