If you’ve been following Boruto until now you would’ve noticed that the anime begins with a beholding introduction, showing Konoha in shambled. Nobody knows what happened, other than the fact that Kawaki had a hand in it. This brings up a shitload of questions which include, ‘where was Naruto during the attack?’ , is he dead? and so on.
Naruto might probably have been transported to another dimension and Sasuke might be looking for him. Boruto meanwhile is the only shinobi capable of defeating Kawaki, hence he’s facing him. This is the most formidable theory one can think of when it comes to why just Boruto and Kawaki are the last standing men.
Naruto’s powers are beyond imagination, even Kaguya suffered at his hands yet many in the fandom believe he’s dead. I too am skeptical about the whole plot but then again, it’s up to the writer to decide who gets to live and who stays.