I can answer it myself after a bit of work, maybe there is someone wondering about similar things in the future:
> (1) will the SolverControl emit convergence although I operate only on some of the DoFs (do I need to reset the remaining ones)
Yes it will. Just reset the irrelevant DoFs and consider only the relevant here.
> (2) are there other options to achieve this (solving a problem on a subdomain such as an interface) using matrix-free
Not sure. However, project_boundary_values works only for serial Triangulations (there is actually an Assertion in deal.II missing). Reducing the overall system size to the size of the subdomain (as it is done for the serial version) while still considering the global coupling of distributed DoFs is exceedingly complicated. With matrix-free, I only touch the relevant DoFs when solving the system and I still have the DoF coupling and ghost value exchange as usual. The only 'price' I pay consists of the additional memory consumption for a global vector in the CGSolve, which is tolerable, or at least the best I can get.
> (3) do you think the approach makes sense or should I just go with the
sparse matrix-vector approach since the overall system will be anyway
relatively small (dim - 1)?
Makes sense. Choosing here sparse matrices is not a good idea as then I would have more unused memory allocated. Also, the (my selected) Jacobi preconditioner might become problematic for sparse matrices, if DoFs on the diagonal are ignored completely.