From the Pathfinder wiki:
In 872 AR, Tar-Baphon discovered a strange thinness between the planes
in the Isle of Terror. After taking over the whole island from the
black dragon Karamorros in 881 AR, he exploited it to dig the
Wizard-King's Pit, a portal to the Negative Energy Plane. With the
island secure, he stored his wealth in Xin-Grafar, filling it with
deadly traps and guardians.
I haven't played the adventure referenced (To Exceed Their Grasp, from The Dead Roads), but it sounds like they are still on separate metaphysical planes, but that the barrier between them is weak on the Isle of Terror, and that somehow exploiting this thinning of the veil required digging.
I'm sure I have a friend that has it somewhere, so if another poster doesn't come in with more details by this evening, I'll reach out and hopefully have an improved answer by Monday.
I found an online copy of an adventure called The City of Golden Death that has this to say about the Wizard King's Pit:
Called the Wizard-King’s Pit, this is the trap Tar-Baphon set for
Aroden, the Last Azlanti, a trap that failed and caused the wizard’s
own destruction. The void descends into the deepest recesses of the
Darklands, where it touches a portal to the Negative Energy Plane.
This portal, forever open, leaks negative energy to Golarion, causing
the negative energy storms and occasionally erupting to create entire
regions of the Negative Energy Plane right here on the Isle of Terror.
So, it appears that the portal is a pre-existing, permanent portal between metaphysical planes that exists in the deepest parts of the Darklands and just happens to be under the Isle of Terror.