Checking in on the app provides you with a known worst case - i.e. the room you choose on the app should be the worst you will be assigned. Checking in on the app doesn't preclude a space available upgrade on arrival at the property. If you're offered an upgrade on the app that you don't want, don't complete the online check in. Either call the property and see if they're able and willing to do something or check in at the front desk and see what can be arranged.