The throughput results will also depend on the number of users in the cell that share resources, not only on the penetration losses that directly have an impact on the SINR values.
If you consider only 1 base station and one user (omnidirectional antenna and no interference, LTE_config.nr_eNodeB_rings = 0), you will see that increasing the penetration loss will result in lower throughput, as we all would expect. However as soon as you introduce interference, LTE_config.nr_eNodeB_rings = 1, then actually the SINR increases when increasing the penetration losses, due to the isolating effect of interference.
In order to have a better understanding you could use a more realistic scenario. I would suggest to use the 3GPP 3D channel model, where you can place users indoor and outdoor, as well as apply a probability to be in LOS or NLOS. You can change the penetration loss for indoor users in the +macroscopic_pathloss_models/TR36873PathlossModel, by giving different values to parameter wall_pathloss.