Do you know about the balanced line standard, AES48?
If you run a balanced phono input, there should be no ground post. Ground should be handled by pin 1 of the XLR. If you see something different, the tonearm cable is likely to affect the sound, which isn't supposed to happen if you do balanced line correctly. If no ground post is present, its a good bet the input supports AES48.
At the output you have a similar issue. AES48 does not allow for dual single-ended outputs since single-ended outputs rely on ground as the circuit return (which is why an RCA connection will buzz like crazy if the ground connection isn't made). Instead ground is ignored (as is should be with any phono connection, which is why ground is a separate wire in single-ended setups; in such cases what is happening is a balanced source is being used as if it were a single-ended source).
If ground is included as part of the signal path the Common Mode Rejection Ratio at the input of the preamp will be degraded. You will also hear artifacts from the interconnect cable. So if you want the most out of the investment its might be a good idea to see if the output of the phono preamp supports AES48.
I think having additional connectivity between the phono section and line stage is a bad thing, but that's me. When I've experimented with this it seems to sound better when the phono section is in the same box with the line stage, assuming the power supply is not a variable.
