As a sales engineer for a dry type transformer manufacturer I have read plenty of specs and have never ran across the tern "safety factor."
The NEC has not interest in the transformer other than it is listed and labeled by a nationally recognized testing agency. Also the they are designed, built and tested per applicable IEEE/ANSI standards.
If the transformer meets UL requirements for example then it is applied and installed per the NEC requirements.
The NEC must be separated from the way a transformeris designed and built. If it is designed and labeled by a nationally recognized testing agency then the NEC alows it to be used.
Safety factor I would understand would be the responsibilty of the person who writes the specs for a transformer. One could consider loads, harmonics, ambient temperature, location, etc. One also considers transformer constuction such as the enclosure, temperature rise, insulation class, and many other things.