I do not use transformers in any of the digital mods. It is VERY hard to physically fit a transformer without removing certain parts that will cripple certain aspects of the DUET or SB3, like full access to all Internet radio or optical output.
I have tried a pulse transformer in my early days of modding the SB2. I removed it after I found more RFI entering the signal path. It sounded quite a bit worse, to me that not using a transformer. The wiring to and from the transformer was acting as an antenna for all the RFI put out by the internal switcher, wireless card and display.
There is even less room inside the DUET to perform any mod.
So far, I have found more audible improvements by using a high quality linear PS than by adding things in the signal path.
I have also found rather large audible difference between different linear power supplies.