How to modify wpa_supplicant.conf
The reason is that Android uses it's own management classes to read/write wpa_supplicant.conf in conjunction with networkHistory.txt file.

The WifiConfigStore in the Android framework does not write entries in wpa_supplicant if not found in networkHistory.txt

I've had success by first adding the network in networkHistory.txt before adding the network via wpa_cli.

However, in general, the usage of wpa_cli in Android is broken by the behavior of WifiConfigStore.