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Separate power supply lets you keep the transformer away from the gain stage, ie no hum. Directly stacked the transformer hum is audible on IEMs at high volume.*
*For some amps.
With good transformer design and good layout, it's really no problem having the transformer in the same chassis--and still have a totally silent design.
When we experimented with two-chassis design at Sumo, we found that many transformers, especially flat-pack or C-core transformers, had more radiated field in the Z-axis than anywhere else. That means, they radiated out the top and bottom of the transformer, mostly.
When our two-chassis stuff was stacked, yep, you guessed it, the field radiating out of the top of the transformer in the power supply section got picked up by the preamp traces in the top chassis, and boom: hum. The same transformer sitting beside the same preamp board had no problems.
So, with the two-chassis products, we had to tell people not to stack them...but they always wanted to.
We experimented with better core material, mu-metal shorting shields, etc, but we were never able to get rid of the hum entirely when components were stacked. When you couple it with the fact that the regulators should be closest to the circuit they're supplying for maximum performance (that is, not in another chassis), we eventually abandoned two-chassis designs.
And this is why we now usually use single-chassis designs, EI-core or carefully wound C-core transformers, steel top subchassis, and careful transformer placement so you can stack, say, an Asgard 2 and a Bifrost, or a Mjolnir and a Gungnir, and not have any hum problems.