1) Kaji and Kaworu's exchange
This is in my opinion the hardest of the instrumentality sequences to explain, but I'll try and give my interpretation.
Anno recently said in an interview (https://twitter.com/scenik8/status/1414165133614407684) that Kaji and Kaworu took over NERV Japan after the Near Third Impact. Visually, the exchange shown in 3.0+1.0 appears to be mostly a flashback to this time period. Kaji and Kaworu appear in Gendo's old office, with Kaworu even wearing Gendo's uniform. Note that for almost the entire sequence the oceans are red (Post-Near-3rd Impact), but only in the last scene does it turn blue and the landscape appears to be revitalised.
Kaji and Kaworu talk about events happening in the present day, but this is likely a mixture of memory and internal exchange within Kaworu's mind. This is similar to how Kensuke also appears during Asuka's instrumentality sequence immediately prior, despite the fact he cannot possibly be there at that time (we literally saw him moments earlier in Village 3). I was also reminded of how in Episode 25 and 26 of NGE, Shinji converses with the versions of the characters inside himself and vice versa. It's possible that at one point during the time Kaji was working directly with Kaworu he invited him to join him and Misato working on the farm he planned to build when everything was over (hence the memories mixed in).
The revitalisation of the world in the final shot is most likely an illustration of Kaworu's intentions post-Additional Impact. Shinji has not yet used the Spear of Gaius to change the world, so it's unlikely this is real. Rather, this is a vision of Kaworu's wish for happiness, which Shinji is hoping to grant. Note that its only when Kaworu goes to reply "Yeah. That sounds nice," that the environment finally changes. I think this entire sequence and conversation is portraying Kaworu relinquishing the role that fate had decided for him and subjected him to countless times, and finally considering himself and his own happiness.
Another key thing to remember is that, in stark contrast with the End of Evangelion, Shinji's main goal in this iteration of instrumentality is to ensure that the ones he cares about find happiness for themselves.
Kaworu: So, Shinji Ikari, what do you wish for?
Shinji: I'm fine. I think I can handle pain and heartbreak. I'm more worried about saving Asuka and the others.
It's debatable whether Kaji and Misato are revived due to Shinji's actions, but that line about joining "me and Katsuragi" definitely does not seem like a throwaway. Once the Spear of Gaius is used, the Evangelion Infinities separate, turn back into people and animals, and fall back to Earth as the world is re-created. This may imply that Kaji and Misato aren't reincarnated as they weren't coreized, but Kaji's line makes me think otherwise. Working with Kaji and Misato appeared to be an integral part of Kaworu's wish, so it follows that Shinji would attempt to grant it. I'm not sure how this can really be explained in-universe though. The Eva Imaginary was essentially another Lilith, so maybe he can just re-create them both?
I also don't think this indicates Kaworu is heading to some kind of afterlife either. Rei and Kaworu leave the studio through the exact same door, which may imply that they're heading to the same place. This matches up with how Kaworu is seen conversing with Rei on the platform. If we assume Kaworu follows through on his wish, this positioning makes sense - regardless of whether Kaji and Misato have reincarnated, their only son also lives in Village 3. Crucially, Asuka, Kaworu and Rei are all on the same platform, presumably waiting for the same train. I took this, together with all the other stuff shown (like Rei's Tsubame doll, Kensuke, and Asuka's entry plug), to mean they will all end up in the Village 3 area.
2) The train station
I don't believe the train station is in the Anti-Universe as some people have theorised. As others have pointed out, Asuka's empty entry plug next to Kensuke's house and the seed satellites are both shown after the Spear of Gaius is used. If we also remember Shinji's conversation with Rei:
Shinji: Another one of you found a place she could call home. I'm sure Asuka will be able to find her own new place as well. A happiness without an Eva.
Rei: That's what I wished for you, Shinji.
S: Yes. So there's a life away from here that you can live too.
R: Really?
S: Yes. I'm going to choose a life without Evas as well. I won't rewind time or revert the world. I'm just going to rewrite the world into one that doesn't have Evas. A new world where people can live.
My interpretation was that Shinji is reassuring Rei that he is going to create a world for both of them as well as Asuka. By extension, we can infer that all of them will be living in the same world, although they may never meet again. Rei also leaves via the same door as Kaworu, which implies that they are going to the same place.
I'll leave out the meta and thematic reasons for why I think the inside of the station is in the same world as the outside/"real world", but another thing to note is when Shinji and Mari are climbing the stairs there is some compositing wizardry being used to almost seem like its transitioning between 2d animation and real-life photography. The fact that the world outside is visible and appears continuous with the inside of the station leads me to believe that this is all the same "world". The station has also clearly been drawn as realistically as possible (except for the route to exit the station as was already noted for story reasons), all of the people outside are also animated... you get the idea.
Basically, I don't think we're meant to read into the transition to live action much other than the fact that the characters have integrated with the "real" world or one very similar to our own.
3) Visions
People have also already pointed out the comparison with the birds shot as Rei and Kaworu disappear behind the train and the Rei vision Shinji has in 1.0. After watching it 10+ times I am convinced that none of the characters are behind the train after the birds take flight, and the train also appears to be empty. I think this is 100% intended to be interpreted as a vision of sorts - one where Shinji is able to reassure himself that the others have found their own way and his efforts were successful before running out into the new world with no regrets.
4) Why did Asuka's entry plug and Village 3 survive Shinji's re-writing?
I think the clue is in what happens during the start of the Additional Impact. As the Eva Infinities sweep the Earth, they are stopped by the L-Containment Field surrounding Village 3. By extension, we can conclude that this area was also spared any changes that occurred from Shinji's Additional Impact. As for the seed satellites, well they're in space so presumably out of the AoE (this is probably why Misato ejected them before the final mission).
Based on his exchange with Rei, Shinji didn't "rewind time" or "revert" the world, but rather he "rewrote" the world. The full Japanese line is actually slightly different in wording to the English translation.
僕もエヴァに乗らない生き方を選ぶよ
時間も世界も戻さない。 ただ―
“エヴァがなくてもいい世界”に書き換えるだけだ
My interpretation is that Shinji saying that he is going to create a world that doesn't need Evas rather than a world "that doesn't have Evas" in the strict sense. I'm taking this to mean he didn't make retroactive changes to the past, but rather re-created the world from that point onwards into one where everyone can live without relying on Evas. This explains why Shinji and Mari appear to still know each other and presumably have memories of all the events, as well as providing more evidence as to why Village 3 and Asuka's entry plug still exist.
As an aside - some parts of the Amazon translation really annoy me because they leave out key details, but that's a rant for another time.
