I always thought that EoE and 25-26 were events that ran alongside one another, with25-26 being shinji's mental battle with instrumentality and EoE being the events that are playing out during 25-26
I never thought one replaced the other, more that both parts make the ending whole
Same.
That's how I viewed them as well.
I'm not sure if it was intentional though, because I've mostly read that episodes 25 and 26 were done that way due to budget restraints.
Either way, I experienced profound catharsis when watching the ending of the original TV series, lol
EoE was the icing on the cake.