Bill Orr makes a similar point in advising caution when putting a filter choke in series with the normally grounded center-tap of a transformer secondary since this point is now raised well above ground potential.
Rodger WQ9E
This is an excellent point. I have a simulation program for designing power supplies.
With a choke input supply, the voltage across the filter choke reaches a peak value approximately equal to the output voltage of the power supply.
Suppose the output of your transformer is 1150 - 0 - 1150 and you use a full wave center tapped circuit with choke input filtering. You would get about 1000 volts DC from the supply.
If you attach one side of the choke to the transformer center tap, and the other side to ground you would end up with a peak voltage on the center tap of about 1000V. The waveform is complex AC, but that would be the peak.
Some transformers like many of the old S series UTC units were designed to have the center tap grounded and you would have trouble using negative lead filtering.
Another reason people put the choke in the negative lead is to enable them to use a choke with a lower voltage spec. But this may lead to trouble also because the transient voltages in a choke input filter are quite high.
You would risk a breakdown in the choke unless it has a voltage spec near the output voltage of the supply.