Both commands correctly reset all the RPG System variables as intended, but do not correctly reset all the gameplay-altering hidden values. For example, with 1 point spent on Inventory Size (increases inventory by 5), using the {reset-points} command will correctly set you to 0 points spent and 1 point available, but you will still have 5 extra inventory slots.
I have observed similar behavior with regards to Logistics Slots and Trash Slots. This bug may possibly apply to all options, but I did not attempt to verify that.