Hmmm at the moment the app only has 16:9 aspect ratio options. So maybe when it tries to set the resolution to 16:9 the games reset it.
If your game uses fullscreen mode, try setting it to borderless fullscreen if the option is available.
If your game also changes the resolution it will override the resolution settings of switch-remote-play, and the stream will not be streaming fullscreen.
I'd recommend making sure your game matches the resolution that is set in the switch-remote-play app.
As for changing the settings in the app, before you connect to your PC, if you press 'ZR' or 'ZL' you can change configuration screens. Go to the 'Encoder Configuration' screen and try changing the Desktop resolution settings there and see if it helps. To change a setting press the 'A' button. If you forget, the top of the screen shows a basic explanation of the buttons.
I hope that helps