Can a toroidal transformer be wired as a common mode choke?
Power line conditioning needs a reasonable voltage insulation between the two coils that make up the common mode choke. If the voltage insulation were not that good, you could get breakdown between the coils and a fire. 

I would have thought that a standard off-the-shelf transformer that has two 6.3 volt secondary windings would not have insulation that is rated to expect a few hundred volts between them. After all why should they - they will likely be isolated from the primary by either distance or some other form of breakdown protection.

In short, you cannot rely on this method - get a proper common mode choke that is rated at the AC mains voltages you use.