I'm sure you already know this, but the game must be in full screen mode in order to use a game resolution that is different from your Windows screen resolution.
The new borderless fullscreen mode takes up the whole screen, but it is still technically windowed, not full screen. So if you are seeing your native resolution which is different from the resolution that you chose in Options, I believe the only solution is to switch to "true" full screen mode.
One other wrinkle that I've noticed, if you use the game configuration app from LaunchPad, you can get the checkboxes into a state where both are checked at the same time, which is not consistent with the in-game Options window. There you have to choose one or the other. If you've used the configuration app, go back and make sure you only have one of those checked.
