If I understand the comments by Rauliruegas, and repeated by Notec and Atmasphere, the theory is that a phono stage that is integrated into the preamplifier is better than one that is separate because the interconnection forms a kind of "weak link". This statement sound generally incorrect. Keep in mind that the signal output from the phono stage should be about as strong as the signal output from a CD player or tuner. I mean, the point of the phono stage is to take a signal that is too weak to be input to the preamplifier (i.e. the signal from the cartridge) and amplify it to a level that is suitable for the preamplifier (there is, of course also the task of RIAA equalization as well). If the signal from the phono stage is weaker, then you probably have a problem of too low a gain level in the phono stage.
An advantage in having the phono stage separate from the preamplifier is that the phono stage is typically the highest gain component in your system, and it receives signals that are significantly weaker than those elsewhere in the system. Those weak signals are prone to interference from nearby stronger signals, so by keeping those signals in a separate box, you can amplify the weak signal while minimizing interference and then once the signal has been amplified, it can then be introduced into the rest of the system.
An advantage in having the phono stage separate from the preamplifier is that the phono stage is typically the highest gain component in your system, and it receives signals that are significantly weaker than those elsewhere in the system. Those weak signals are prone to interference from nearby stronger signals, so by keeping those signals in a separate box, you can amplify the weak signal while minimizing interference and then once the signal has been amplified, it can then be introduced into the rest of the system.