Achievements never pop up for me if the game is unfocused, basically the game bar overlay needs to be active on the game and also seeing that you are playing; I noticed that the start up screen of some games on the xbox app sometimes leave the game unfocused if it's running in borderless fullscreen.
Best thing you can probably do is use your mouse to click in the game's screen, and then using the game bar shortcut to open it and then close it.