Separate windings for separately derived sytem means separate circuits for primary current and secondary currents, other than whatever point is somehow connected to ground. Arrangement of grounded conductors for NEC applications normally means that a grounded conductor should only carry primary or secondary current and not both in normal operation. Is ok if it would happen to carry fault current in an abnormal situation.
What is not a separately derived system is an autotransformer. Those have a common conductor that carries both input and output current simultaneously during normal operation, and the "coils" are in series in some way rather and are not limited to just magnetic coupling through the core being the only interaction between them