scripts: runners: nrfjprog: Use --tool-opt in all operations

Pass on the tool-specific options to nrfjprog during all operations, and
not only when programming. This is useful when combined with options
like --ip, that allows west flash to be used over the network.

Fixes #55340.

Signed-off-by: Carles Cufi <carles.cufi@nordicsemi.no>