The Finale makes me think jack + zoe are dead (here is why)
I think jack and zoe never made it to the "real" eureka and bought the farm on the road going there and here is why:
1st: the reason for the two versions coming and leaving eureka seeing each other is never truly explained.
2nd: It could have been a "closed curvelike timeline" involving all of their lives in eureka across several alternate dimensions(starting in the original universe and ending in post-Dr grant universe)but what kind of device in either "eurekas" would be that powerful or effective to do such a thing without destroying those universes especially if it was a unintentional "accident" in all those universes.
3rd: the happy ending nature to the whole ordeal jack found a smart, loving, hot wife and zoe found a great brother and a boyfriend not to mention that both developed great friendships there and an awesome life in eureka with everything moving in their favor; Oh allison is going to marry another man? just let the universe unravel to solve that problem and bring her back to your arms sheriff carter, the town is going down? here comes Dr. grant to the rescue, zoe is not doing well in school? nothing that a dimensional switch cant fix. Its just too convenient to not be "heaven" their version of it anyway probably they imagine the place as "eureka" because they still dont accept they are dead which would explain why they see themselves leaving and returning to the town after a certain time there.
4th: it would explain certain things about the series-town like the 2nd episode titled "many happy returns" where a dead woman appears to come back to life (an idea by the way used up to the very end see Dr. holly marten)of loss and renewal
Dr. Noah Drummer and those christmas episode specials like "Do You See What I See" the possibility of area 51 and those amazing artifacts actually existing (feels more like the imagination of an ultra smart comic book fan teenager running out of control)
5th: carters journey into the "wormhole" in the final episode felt a lot like a near death experience where people remember or see their whole life passing by their eyes.
6th: the fact that eureka had smart enemies that could have killed them before they got there in the first place. (yet conveniently did not)
I know its sad but they would not be the first ones to try to pull off a similar twist see similar offenders Quantum Leap and Lost