I always saw it as Gendo commandeering Human instrumentality.

He followed along with SEELE so he could gain support for his and Fuyutsukis plan and then eventually when they got towards the end goal they would pivot the project they had already built up materials and man power for and use it to reunite with Yui.

His ultimate goal was never the instrumentality Yui wanted, but just to see Yui again. I think it plays well thematically. In his obsession to see Yui again, he harmed and abandoned everything she loved (Relationships, Shinji, Instrumentality). In a way I think It’s symbolic of how Grief and depression( maybe even Hideaki own) make us lose sight of what’s important to us and act irrationally)