It depends, an iPortal lets you send trains to other users via the internet. While the other portal lets you send trains to other parts of the route.
Example: I set portal1 at the est end of my route, I then set portal2 10 miles tot he west. I can the run a train from the east portal through to the west portal with out using the track in between. Or with an iPortal, I can name it Jib123 and tell it to send to user tallboy22 portal boytall. Then I can send a coal train to your route and unload coal. And visa versa.
I am working on a route that uses to linked portals that Ii will soon be putting on the DLS, so keep an eye out for it and you can see what I mean.