End of Evangelion is the proper ending, but i prefer to view the ending of the TV series as them all staying orange goo with human instrumentality and Shinji coming in terms with having no physical presence in the world.
I've always understood the 2 versions of the ending to be the same events from a different perspective. With end of eva showing what happens in the physical, and the tv series 25-26 focusing on Shinji's personal journey inside his own head, which if you overlay them on top of each other, is him making a choice to leave the LCL sea, accept himself, and be an individual again, hence the congratulations. I don't really have a solid grasp on the motivations of the final EoE scene on the beach though (which I place post-congratulations). I'd love to hear some director's commentary if one exists. I need to do a full series and movie rewatch. It's been a few years.