Preference for separate phono stages?

Paul, don't you own a Shindo preamp? If that is the case you answered your own
question - it's all about the design and the implementation (and maybe some
added flexibility for separates).

Most external phono stages are better than internal ones just because more
development effort is spent on the phono stage. However, there are excellent
internal phono stages that are well designed and that are difficult to beat with
external ones (for example Shindo and Vacuumstate preamps).

To contribute some more to this topic:

The best people to ask are designers of full function preamps on why they choose a single box solution. Talking to Allen Wright, he thought the main advantage was that one could avoid one more gain/buffer stage and the interconnect when combining pre and phono. According to Allen the problem with separate phono stage solutions is that they should be able to work with a variety of different preamps, requiring different driving and impedance-matching capabilities.

Finally from a noise perspective, I don't quite see the advantage of a separate case. One could always separate out the phono stage in a different shielded section of the preamp and keep paths to a minimum. The only thing that may be worth putting outboard seems to be the power supply IMO. I don't think that putting everything into separate cases is ideal, simplicity and shorter signal paths can have their own advantages, thus a single box solution doesn't necessarily mean a compromise.

Of course, the biggest advantage in separate phono stages IMO is the flexibility. Not only do you have more flexibility in matching pre and phono separately, but most external phono stages have more loading options too.