Currently, for ease of commissioning on both App platforms (Android/iOS) we use the commissioning flows provided by the Android (technically Google Play Services) and iOS. These frameworks take care of all initial onboarding, talking to the device via Bluetooth and setting up of the Thread or WiFi network configuration.
I’ve outlined this a bit more in detail in the Matter Pairing/Commissioning hints thread here in the community forum.
So all the above are essentially limitations/implementation details of the Google Matter implementation. They are very much focused on ease of use and expect a flat/single network which most of their users have.