Here's my take...

I have to agree with you. I really think the trio(E2, S1, S2) hatched a plan, while E1 was on the computer looking for the folders, so that they all will be with whom they want to be. As S1(considering S1 pretended to be S2) said, "A lot happened last night after you left." so maybe that's what happened.

I think the whole plot is more devious than what you've described.

Based on the computer files we hear, with E1 listening to the couples trying to perfect their voices, and based on what S2 tells E1 about them not being able to leave the guest house and the fact that this curse is now passing on to the 1s from the 2s and how E1 does find himself unable to exit the guest house... my take on it is that each couple that comes to the retreat gets stuck there with the previous couple taking their place in the "real world" and taking over their identities.

I don't think that there's an alternate dimension going on with different versions of E and S; I think that the previous couple that vacationed there was stuck in the guest house and have been trained to take over E's and S's identities. Obviously, there's still something magical or extra-dimensional in regards to the explanations of how this happens... but I don't think it's as simple as an E & S from two different dimensions, more that it's a pass-on-the-curse kind of thing. The previous couple gets their release from being trapped in this "phantom zone," where they've had to exist almost as spirits haunting the place-- unable to leave, and with periodic manifestations initially based on which of the new couple is entering the guest house. As the weekend goes on, normally the previous couple is supposed to set the newer couple against each other, and the new couple ends up trapped in the guest house while the previous couple escapes into the real world with their new identities.

If this were to play out as it has in the past, my theory is that E2 and S2 would have left together, and E1 and S1 would have been trapped in the guest house together. Eventually, Ted Danson would have showed up and given them new identities of a couple planning on coming for a weekend, and trained them to talk like them. They (E1 and S1) would have then eventually escaped back into the real world in new identities, glad for some way back into the real world, even if it would have been as different people.

But in this scenario, E2 decides he likes S1 better, and that he wants to leave with her instead of with his wife/S2. This culminates in an ending similar to what you've described, where S2 warns E1, and then E2 runs into the force field and E1 thinks he's leaving with S1, believing that S2 is at the side of the road with the injured E1. But of course, S2 has tricked E1 and left with him, and he's accidentally left his actual wife/S1 behind... which is fine with her as she's already decided she prefers E2 anyway. But she's disappointed that ultimately E1 can't tell the difference.

I think the bacon thing is the giveaway that it is in fact S2. Because E1 never told S1 about the bacon, so she wouldn't have known to make that specific change to fit his "needs," and he never mentioned the conversation to S2 either, so she wouldn't have known not to cook the bacon to preserve her cover as S1. But I think in that last dark moment, E1 finally realizes he's now with S2... and he accepts that he's happier now, and accepts the outcome. I don't think he believes it's S1 and she's made a decision to cook him bacon to preserve the now-happier marriage.

Ultimately, I believe this movie is a pretty dark take on the fact that people often marry their idealized fantasies, and when faced with the opportunity to accept the flawed person they married when they finally see that person for who they truly are... they would prefer to return to the fantasy. It's like the Joey Pants character in The Matrix deciding he'd rather turn a blind eye to the fact that he's living in The Matrix and not in reality simply because he enjoys that reality more, even though it's a fantasy.

As you say, it is left ambiguous to promote thought and discussion, and to allow people to have their own interpretation to some degree. That's mine.

It's definitely a very clever and well-executed little indie, and it's refreshing to see something able to do so much without being dependent on a huge studio budget, and to simultaneously tackle relationships from a very complex perspective.