The app manifest basically contains metadata that allows the browser to treat the game like an app. It contains information like the title, icons and orientation lock. Right now browsers mainly use it on mobile for the "Add to homescreen" feature to create an app icon, but it might be extended to be more app-like in future. It is entirely optional so you can remove it, but then browsers will treat it more like a web page and less like an app.
I don't know why this feature would ever be a problem. The app manifest is an ordinary json file and all the server needs to do is send it like any other file and it will work. I can't offer more advice without knowing exactly why this is a problem for your client.