Honestly, god only knows. We've been burnt by rumours too often here to assume it really will come to Prime. The Latin American rumours, and the accompanying release schedule that involved the first three rebuild films, have so far been nothing. Maybe something will materialize later on, but I'm not trusting anything right now.
Amazon Prime streamed ep. 1-26 of NGE itself in Japan prior to Netflix getting the global rights for the the series, so it wouldn't be unprecedented for Netflix to buy up something Evangelion related globally (including in Japan) to stream on their platform. Khara is not afraid to switch their streaming partner, both domestically and overseas.
We'll have to wait and see.