Theory and Analysis:Motherly and Cross Symbolism in EoE

Incidentally, supplemental material like Groundwork of Evangelion directly associates this scene with Yui

After deploying in Eva-01 and seeing Asuka's dead Eva, Shinji panics from the shock of losing yet another person he cared about. To assure that the process of Third Impact will continue, Lilith morphs into Kaworu. This calms Shinji down, and Lilith uses the opportunity for the Lance of Longinus to penetrate Unit-01's core and transform Unit-01 into the Tree of Life.

Shinji's easily missed vision of breasts when Yui asks what he wishes for

Immediately afterwards, Yui explains that "this Rei represents your very hopes and dreams"; as she says that, Lilith morphs back into Rei. Rei then asks Shinji, "What do you wish for?" Shinji has a vision of a woman's bosom, and then the screen has a "bubbly" effect and turns orange, much like LCL. This is when Shinji enters Instrumentality.

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  Storyboard explaining the scene and the easily missed "woman's breasts"...

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  ...followed by the "waterdrop" motif that is used repeatedly in the series to allude to Yui inside Unit 01, including in the opening.

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  The sandbox scene immediately afterward, with a toddler Shinji making this more explicit. Notice the "woman's breasts" as hills in the background and how he is on top of a symbolic womb.

This depiction of Instrumentality is focused on Shinji's return to the womb and his anxieties about the women in his life, mainly Asuka, whose affection he desperately and selfishly seeks immediately after entering Instrumentality. Moreover, the whole sequence is backed by the music track "Escape to the Beginning", yet another reference to the womb.

Later, Rei-Lilith asks Shinji if he wants to "become one in body and soul." New sexualized images are again shown from Shinji's POV, as per Groundwork.

Shinji says, "You were there all along," echoing what Asuka says earlier in the movie when she finds out Kyoko is residing inside Unit-02, and Shinji sees Misato's cross, his last memory of yet another maternal figure. Both Asuka and Shinji quickly revert to a status of childlike glee. Shinji is looking for an escape, a mother's embrace to let him run away from the harsh reality.

Interestingly, an earlier draft of EoE made this far clearer, emphasizing further (to Gendo) that Adam has been fused into Lilith, as well as her trying to penetrate Unit 01's core.