Low Voltage Transformer in Subpanel?
You are correct.

There are several points in Article 725 that are not going to allow that to happen.  This would give you no viable plan to rigidly separate mains from low voltage wiring, and that won't do.  

Further, it would violate NEC 110.2 and 110.3(B) because you'd be defeating the UL-approved enclosure design, and using the transformer contrary to instructions and labeling.