What you describe is the behaviour with passthrough = true, but it should default to false.
The kalman filter component is based on this code:
Regarding the estimation of Qk and Rk you are pointed to this:
One practical approach to do this is the autocovariance least-squares (ALS) technique that uses the time-lagged autocovariances of routine operating data to estimate the covariances. The GNU Octave and Matlab code used to calculate the noise covariance matrices using the ALS technique is available online under the GNU General Public License .