From my point of view, the series diverges into two separate continuities from Episode 23 onward (however, the argument could be made for Episode 22 being the divergence since that’s where we start to get the Director’s Cut episodes).
Physical Evidence:
We know the Loop exists, as per the ending of "Evangelion 3.0+1.0: Thrice Upon a Time" and other minor moments in the Rebuild series. In regards to the original series having multiple timelines, there are some key differences between the On-Air episodes and Director's Cut episodes.
The most important change between the On-Air version and Director’s Cut is the entire sequence of Rei vs Armisael, which ends with Rei’s EVA turning into Lilith-Rei before exploding in the DC. Following that, in the same episode, we see Terminal Dogma and the EVA graveyard both look completely different that their On-Air version. There’s also double the amount of Rei clones in the tank in the DC compared to the original counterpart.
I think it’s important to remember that the Director’s Cuts were made using footage that was created for the theatrical film “Death and Rebirth”. The film was made to promote EOE and due to that, a lot of scenes were reanimated or changed to fit the “new” narrative end of the series that would later be released.
On the topic of "End of Evangelion," everyone knows that it was meant to be an alternate ending to the original series, while being complimentary to the original ending. The two most important differences between 25 and 26’s ending vs EOE are the titles and Misato’s death. A lot of people believe EOE is what’s happening in reality while 25 and 26 are during Instrumentality but I don’t necessarily agree with that.
In the original series, we see a glimpse of both Misato and Ritsuko’s bodies during Instrumentality. However, in EOE, by the time Instrumentality starts - Ritsuko had already turned to tang and Misato’s body was blown in half.
Then we have the title-cards.
Let’s compare the original series title card to it’s counterpart in EOE
Episode: 25 - Do You Love Me?
Episode: 25’ - Love is Destructive
Both of those titles are very clearly linked but what’s interesting is the use of the apostrophe symbol. In mathematics, the apostrophe symbol shares a resemblance with the Prime symbol - which is used to denote a derivative, transformation of the original form or can be used to show that it is a set Complement (ie, complimentary).
In music, it’s used to show it being different from it’s original form - “If it is very much like the A section, but with some important differences, it can be labeled A’ (pronounced “A prime”). The A’ section can also show up later in the piece, or yet another variation of A, A” (pronounced “A double prime”) can show up, and so on”.
Was this intentional? Probably not but it is in the Japanese titles for the Rebuild films and Kotono Mitsuishi specifically calls attention to it in this interview - https://wiki.evageeks.org/Evangelion_3.0%2B1.0_Assorted_Translations#Mitsuishi_Kotono_as_Misato_Katsuragi
"This is probably the conclusion of Evangelion, but the name of the film does have that little repeat mark in there, doesn't it. [Laughs]"
Maybe I'm reaching but it certainly is a great case of confirmation bias. Regardless of all of that, what do I think the continuity looks like?
Taking into account “Death and Rebirth” and “End of Evangelion” being connected as pseudo-duology, it looks something like this
Continuity 1: Neon Genesis Evangelion Episodes 1 - 26
Continuity 2: Neon Genesis Evangelion Episodes 1 - 21, Episodes 22 - 24 (Director's Cut), and End of Evangelion
Outside of the major differences I’ve brought up, there are a lot more minor continuity differences that you can see here - https://wiki.evageeks.org/Director%27s_Cut_Episodes
Most people that watch the series on a platform like Netflix might not recognize this theory’s general idea because Netflix uses the Director’s Cuts in place of the On-Air versions of 22-24 with the original episodes 25 and 26 following them (in theory, merging two potentially different timelines into one). Personally, I don't like that the original episodes 22-24 have been essentially disregarded.
Anyway, while none of this was probably intentional and is probably a lot of reaching, I feel it makes EVA as a whole feel more connected and interesting to think about. Let me know what you all think or if you have your own theories!