In the case of the VanMoof s3 and above the app is used to unlock the bike. It has a “kick lock” that basically locks the rear wheel. When the phone approaches the bike then they communicate via Bluetooth and allows the “kick lock” to release either by pressing the button on the handlebar or tapping on the app’s button (or watch app companion).
Apart from that it allows to change some settings that are not configurable on the bike. The bike has only 2 buttons and an LED display. Useful settings are for example the speed profile for the automatic gear shifting.