Current version of Aurora: 1.9.1
At the moment, I'm unaware of any method of setting the window size for full screen or windowed mode, when using either the Aurora compatibility mode launcher, or the SteamTinkerLauncher for the forked Aurora.exe application. The experience, when not defined, launches the application in the smallest form for width and height, which makes it difficult to navigate, or to select options in games for, often cutting off text to know what the option does.
I'd like to see optional command line arguments for window width and height, so users can set the resolution themselves to match either the steamdeck resolution at 1280x800, or to the device they're connected to.
In the setting in arurora there is a setting to launch in maximized mode. I don't remember exactly where but it's a box you can check just read them and it should get you there.