What about portals having slots, like chests, but that only accept ore. And you need a certain amount of ore, like a full stack, in both sides to be able to transport through it.
For example, you need a full stack of copper ore in both the departure and arrival portals to be able to transfer copper (ore or ingots) through. Or a full stack of silver on both sides, etc.
This means that you need to transport at least once without portals in order to load both sides. It also means there's a cost to using the portals. You have to decide if it's worth 60 silver to be able to transport additional silver, or if that 60 silver would be better used to craft/build. Or, you could use the 60 temporarily to transport a greater amount, and then remove it in order to use it, but then that portal can no longer be used for that type of ore until you refill it.
I don't want to re-litigate whether or not portaling ore should be allowed. If your solution is either "just sail the metal everywhere and don't portal it" or "just cheese it by using a second world" then that's great for you! This is just an idea for how it could work in the base game while adding a cost and maintaining a bit of challenge in doing it.