I agree that the game is probably another world, but I don't think they're gonna merge, or that anyone other than Kou will become their game character. Why have the science-y pod thing from the 1st chapter restructure Kou's body if the whole world was just gonna have that done automatically when the worlds merged anyways?
I'm not sure if the manga or LN is going to go in a different direction entirely but the Web Novel on which both are based on, does make clear reference to the Author's previous work, to which Destiny Unchained Online is a shared universe sequel. That story is Worldgate Online, and DUO in its set-up chapters clearly refers to the "Worldgate incident", and that DUO is leveraging much of the same technology pioneered to create Worldgate Online.
In Worldgate Online, the world was also made very realistic, though rather than being another world, it was closer to a simulation of another world, that of the origin world of the game and technology creator. There is a supernatural element though where a ritual intergrated into the game, leveraged to enable evolution and newgame+, affected the players real world selves, and when a certain goal was met, all evolved players were transferred into the game's origin world as their game selves, creating the worldgate incident.
The purpose of the game creator, among a few other goals, was to recreate an extinct rare species vital to the survival of his origin world, through the evolution ritual.
The DUO producers, as far as I can tell in the Web Novel appear to have gathered staff from the original Worldgate Online project, but the purpose appears to be quite different