The theory that deals with Neil moving backwards the whole time make no sense, it's a complete shot in the dark. Any backward moving person will unable to communicate coordinate with a forward movie person.
When one is inverted, they need inverted oxygen to breathe. For the first time The Protagonist inverts we see him wear the mask. In every scene of the movie if we see people with masks, that's our visual cue that they are inverted.
In the end, The Protagonist saw a dead inverted man who took a bullet for him. On seeing the ring on Neil's bag, The Protagonist realizes that Neil is going to go back, invert himself and go back to the location of the bomb. Over there he will get killed.
Neil is walking away to his death. The Protagonist knows this. Neil has also guessed this. Which is why he says "It's the end of a beautiful friendship for him".