Hello Sven,
The Thompson boundary conditions are based on the theory of Riemann invariants for the Saint-Venant equations. The idea is to solve a linearised Riemann problem at the boundary, taking into account: 1. the exterior state -> what you want to prescribe, 2. the interior state -> coming from the computational domain.
So I don't think you can "force" a water depth with the Thompson formulation. The bathymetry change must modify the solution inside the domain, which yields different behaviour at the boundary...
I don't think the partitionning has an influence on this, it would seem surprising to me.
So I don't really come with a solution for you...
By the way, we tried a similar thing for a simulation in the Pacific Ocean and got instability issues too. Using Thompson in our case (where the fields are considered as constant on the vertical), while the water depths were very important with velocity/temperature changes only very close to the free-surface did not seem adapted. What HR Wallingford tried was to prescribe the velocities from the other model at the boundary, and then do a smoothing between the boundary and the interior on a certain width (they called it sponge layer). However, this kind of solution is not conservative and we could probably improve it.
This kind of problems is far from easy to treat and worth investigation. I think quite some people working on oceanic simulations have proposed approaches to prescribe boundary conditions coming from other models but I don't have much experience on this topic...
If you want to know more about this "sponge layer" approach, I have an svn branch with the code for it, and you can ask Sébastien Bourban about it too, he developped that approach.
Best regards,
Agnès