The use of such pads, as well as the use of 'flex' for connecting the conduit, is a trade practice and nothing more. It is documented in NECA workmanship standards.
That said, many transformers already have vibration isolation pads built into them; typically there are some bolts inside that need to be loosened as part of the installation. In that instance, you could argue that manufacturer instructions required you to loosen them- even though the NEC itself has no requirement for isolating the transformer.