It does make sense from a gameplay perspective, because it disincentivizes the player from taking a load of stuff out of the storage of their colony and dumping it on their own open market.
Without tariffs, you could even do this from resource stockpiles if you needed money NOW rather than at the end of the month - you could take potentially tens of thousands of resources, pay for them later, and get the money now. (You can in fact still do this with tariffs, but you know you're taking a solid chunk as a loss later.)
If the trade price for that resource ever went even a credit above the 'nominal' price (which, admittedly, is rare for many resources - but it does sometimes happen) then this would become the optimal choice. Pull every unit your colony can provide, and sell it back to independent traders or whoever Commerce markets represent, and you've got free money for clicking some buttons.
Narratively, tariffs make no sense, but they have a strong gameplay reason to exist as effectively a money sink to prevent players from generating money from nothing with short term economic conditions without ever stepping foot into a spaceship. Sure, you can do it by creating a shortage and doing some black market trading or whatever in the core worlds, but now you're interacting with a lot more game systems (patrols, simulated economy, transit time, cargo space limits etc) and so it's much easier to argue that it's generating good gameplay.
Perhaps they should be reduced on player colonies, but given a different name - overhead, bureaucratic inefficiency, networking fees, whatever.