@javier.nr
Turns out, it is not a problem with RUI3 or with WisToolBox.
It is my spoiled brain that forgot that RUI3 is different to my own WisBlock API 
Try this for the responses of the custom AT commands:
if (param->argc == 1 && !strcmp(param->argv[0], "?"))
{
// Send over UART/USB
Serial.print(cmd);
Serial.printf("=%ld\r\n", g_send_repeat_time / 1000);
#ifdef RAK4630
// Send over BLE
Serial6.print(cmd);
Serial6.printf("=%ld\r\n", g_send_repeat_time / 1000);
#endif
}
In RUI3 the ATC command handler is sending the response by itself, so if required to send over BLE, you have to add it. Send with Serial6.print…
Didn’t find time yet to test it fully.