I think the ambiguity here stems from the preceding sentence using the word "system" twice. Here's the start of the section (2017), where I've labeled the two uses:
250.20(B) Alternating-Current Systems of 50 Volts to 1000 Volts. Alternating-current systems (Use 1) of 50 volts to 1000 volts that supply
premises wiring and premises wiring systems (Use 2) shall be grounded under any of the following conditions:
(1) Where the system can be grounded so that the maximum voltage to ground on the ungrounded conductors does not exceed 150 volts.
So if the word "system" in paragraph (1) refers to Use 2 in the opening sentence, then you naturally get the interpretation you have proposed. In fact, you could take that to an extreme and argue that you are not allowed to use a transformer with a 240V 2-wire secondary, as such a secondary could be center-tapped to satisfy 250.20(B)(1).
While if the word "system" in paragraph (2) refers to Use 1 in the opening sentence, you get the interpretation that Larry and I favor, where the "AC system" is defined by which circuit conductors you choose to bring out of the transformer to supply the premises wiring system.
Cheers, Wayne