I have a server with a world for Spawn, a PvP-Factions world, and a "safe" (no-PvP) Survival world. Using the directions given, I created a world called Survival, and a world called Survival_nether. According to the main MV-Nether Portals GitHub page, they should auto link. They do. However, a portal is not created in Survival_nether when traveling through a portal in Survival, and vice versa. In addition, portals will not link to each other, meaning that if I (for example) create a portal in Survival, travel through it to Survival_nether, and create another portal a few blocks away, it does not link with the original portal.
I have seen other tickets with this issue, but it seems they have not been updated with the latest information nor a fix from the development team.

this has been covered in #68