Because those describe the as-wired connections of a dual-secondary, dual-voltage transformer, not the physical characteristics of the construction of the transformer. A POCO transformer, for example, can be configured with the dual secondaries wired for 120/240v 1ph with 3 wires out, or 120v as part of a 208/120 3ph wye with 2 wires out.
A genuine single-voltage 2-wire secondary can not be configured for anything except a single voltage because there are only two wires. Even a center tap on a single winding means the transformer does not qualify as a single-voltage secondary with only two wires. To me, the construction, not the field connections, describe the transformer.
Now, I am not claiming to know which example they had in mind when the code was written. I don't know whether the wires "brought out" of the transformer is what determines the characteristics of the transformer.
Added:
"Conductors supplied by . . . " is not the same thing as conductors used. It says "a single-phase transformer having a 2 wire (single voltage) secondary." It does not say "as long as you're using it as . . ."