Chrome browser is only 50% of Electron. The other 50% is a complete nodejs distribution which allows access to the OS filesystem, network, anything Java or .NET can do on a desktop... So no, it's not just a browser web app. Electron is absolutely native to the OS is runs on.
The only reason it's got all those permissions is because it is a native app, which can claim all those permissions. Sure, Electron app are browser wep apps marketed as a native application, but by definition, native apps can do everything Electron apps can do.