Equinox is a mess. The only thing their experience shares in common is being pulled into the Delta Quadrant by a being called the Caretaker. From there, their experience diverges. Voyager encounters the Kazon, Vidiians, Talaxians, and the friendly Sikari, meanwhile Equinox encounters the Krowtonan Guard, whom Neelix has never mentioned (the Mikhail Travelers in "Darkling" warned Voyager about a different dangerous group ahead, whom they avoided). Meanwhile, Voyager encountered the Borg or Borg-affected worlds & people a few times while Equinox somehow completely avoided it. How can Equinox avoid all the races Voyager encountered for est. 1000+ ly (Seasons 1-2)? How can Equinox avoid the Borg who occupy a huge swath of the quadrant and have transwarp conduits increasingly intersecting the middle part of the quadrant. Meanwhile, Equinox got the death dolphin summoning device from the Ankari. They claim to have cut decades off their journey that way, yet Voyager finds the Ankari, what was it, just 50 ly back. As I said, a mess.
I've wondered if the Equinox crew were so traumatized, they're hallucinating, as delusional as the "Bliss" affected Voyager crew, thinking they're traveling far, but really they just have conventional warp and crawled 50+ ly with their dolphin-unsafe fuel, being too psychotic to notice their sensors/odometer are damaged. That and the Equinox being pulled into Season 5 space (like say the space right before Voyager arrived after "Dark Frontier"'s jump) by another being called The Caretaker, who is either not a Nacene or was another Nacene who committed the same mistake and stayed behind to care for the world he FUBARed is perhaps the only way to smooth over the gaping geographic plot holes in the episode. "Equinox" is a fun story to try and make the most sense of. Or maybe they did find a wormhole close to the Array, though one would think well-traveled Neelix would've known about it.