Thanks for the reply, thought it's an outdated answer. I took a look a the source and well there are only 227 lines (previous answer called for changing lines 252, 253, and 254). However I found my answer. There are 3 calls to begin:
- int begin(char* ssid);
- int begin(char* ssid, uint8_t key_idx, const char* key);
- int begin(char* ssid, const char *passphrase);
I was setting the passphrase in the example sketch and that was calling into wifiSetPassphrase, which overrides the wpa_supplicant. So the answer is, don't set the passphrase if the device is configured to automatically start the WiFi connection.