[fix][nonequilibrium][tests] fix gradient calculation in nonequilibrium

This fixes a bug introduced with !1517 (merged) and thus fixes the test_mpnc_kinetic test. However the newly introduced 2p2c test references were created with the buggy code and thus have to updated (in this patch). We make it more robust by increasing the Newton accuracy, introducing checkpoints and incresing the initial time step size, which results in many less time steps.