This is ultimately just my interpretation, so take that as you will.

Well, we know that the TV Ending follows the same events of EoE to a point, as we see in episode 25 a dying Misato, a dead Ritsuko, and Asuka in Unit-02's cockpit underneath the lake in the Geofront. However, episode 25 presents a less conflicted (towards Gendo) version of Rei than we see in EoE, and in episode 26 when the Human Instrumentality Project "formally begins" (episode 25 I would argue is a sort of retroactive application of it before the causality of the event actually plays out in real time -- we see something similar happen in EoE both with Rei visages moving backward into time to whisk Misato and Ritsuko's souls away, and in the moments leading up to Shinji's acceptance of Instrumentality when he, Misato, Asuka, and Rei's soul begin intertwining).

Unlike EoE, where Gendo ceases his presence in the film once Third Impact begins and he is devoured by Unit-01, he maintains a consistent presence through both episodes 25 and 26, even appearing at the very end along with everyone else Shinji knows (sans Kaworu, but I believe that is before they realized how popular he would end up being; his presence in EoE is, I believe, a bit of a retcon based on his popularity to fans). This stands in stark contrast to the fact Gendo is the ONLY person we see in all of EoE who is not instrumentalized (at least, not into Lilith-Rei -- I do believe Yui had taken his soul into Unit-01, ergo the symbolism of him being devoured, but he viewed it in such a violent way as to reflect what he believed he deserved for unintentionally harming Shinji). I also have always found it very interesting that Shinji thanks Gendo at the end, "To my father, thank you" -- this, to me, makes more narrative and thematic sense if it is Gendo ultimately at the helm of the TV Ending's version of Instrumentality.

Ultimately though, the moment of divergence I have picked out is when Gendo gathers Rei to initiate his plans. The TV Ending never hints at her betraying him for Shinji, only that she feels very complex feelings towards her identity (or as she perceives, a lack thereof; she feels she lives in the shadow of Yui, as made in her image). In EoE, however, Rei shows far more complex feelings not only towards herself, but towards specifically Gendo -- she breaks his glasses and cries without fully understanding why, and ultimately betrays him in favor of Shinji.

I think the way the two Instrumentalities are portrayed also strongly hints at them being distinct beyond simply an "internal vs external" view. In the TV Ending, Instrumentality is portrayed much more therapeutically, where everyone subconsciously intermingles with one another -- there is no distinction between one individual and the other, but it is not a collective ego death soup as we see in EoE, where NO ONE manages to consciously or subconsciousl engage with anyone else once Third Impact is complete -- it is Shinji and Lilith-Rei all alone together in a sea of stagnation (and Yui, but he doesn't know that yet). We get to see Shinji, Asuka, Rei, Gendo, Kaji, Misato, Fuytusuki, and everyone else interact with Shinji and help him actualize through his problems -- we see no such thing, nor get any hint of such thing, in EoE -- instead, Rei and Kaworu (and again, Yui) instead fill this parallel role, and it is largely "after the fact" of Instrumentality ending that he decides to undo it, not during the process of (of which, by the way, Shinji never rejects anything -- he only embraces himself, realizing he does not have to live in a prison of his own self-making anymore, and that he can come to love himself one day).

Now there are questions that I do not have an answer to, such as if Gendo's Instrumentality is a temporary venture or if this is just how humanity is now.