I think it partially comes down to the manufacturer's approach to internal screening, and probably also filtering as well. Rega amps have no output filtering, and particularly in the case of the Brio-R everything is packed tightly together in that small box without screening hence the propensity towards some noise. If they added a DAC chip into that recipe it probably wouldn't be a good idea, and so in amps like Regas the seperate amp and DAC approach is probably the best.
Japanese manufacturers are rather more fastidious in their screening and isolation. For example, Marantz screen the DAC sections in their integrateds to avoid them interfering with the rest of the amp, and on the PM7005 they even have an 'analogue mode' to switch the digital circuits off when they are not being used.
Just a thought, and I'm not suggesting one is better than the other, just different!