I think the key to unlocking the tunnels is the Nightvision perk. I was just reading the description which says:
"Exploring the underground tunnels beneath Moonwood Mill can lead down to a dark dead end. With this ability, Ava will be able to conquer them by seeing things she would otherwise have missed, as well as spend less time hunting for prey at night"
I tested it with Rory since she already has Nightvision, and after 5 trips starting at the sewer grate she unlocked the route from there to the portal potties. I tried several more times starting from the potties but didn't discover the route to anywhere new. Using that example, I had Rory go home and try the portal there and the sewer grate was greyed out and the portal potties weren't even an option. It seems like having that perk is either necessary or at the very least it speeds things up, and you have to start from each portal and through trial and error learn the way to one of the other exits. Learning a new exit point doesn't grant you the ability to go there from just any portal. You have to learn how to find that exit from each of the other entrances separately.