AKAGI:“It doesn't matter if you die, you can always be replaced.
Rei...
The same as me.”
RussianRiz: Ah, the choking. Certainly something significant in the franchise. The rejection of the other. In this case, Rei 1 resembles Yui directly, which is why Naoko attacked her.
UrsusArctos: And what a powerful rejection of the other this is! Along with Shinji choking Asuka in End of Evangelion, we have Eva-01 choking Eva-03 and breaking its neck, and Kyoko breaking the neck of the Asuka doll before hanging herself. The black silhouettes on red evoke violence very powerfully, and are seen again when Asuka finds Kyoko hanging. Naoko's comment is creepily appropriate for Rei - who literally can be replaced if she dies, and her second incarnation uses Naoko's very words - but also for her daughter, Ritsuko, whose own actions land up with her being replaced by Rei. There's a whole cycle of tragedy and irony woven into Naoko's statement here.