I'm not a 456 guy but I've perused many threads which discuss the pros and cons of the 456.
First this I have to ask is did you get, or are you getting, a PPI. The newer 456's have fewer problems but this is definitely one of those cars where a PPI would be essential. Some of the newer models you can get away without one (a la 360, 430) but there's enough historical data available to know that a PPI is a must. It pays to educate yourself but a professional's eye is maybe what you need.
Ok, that being said, I think the leather shrinkage is almost expected to some degree. As for price, if the car is is good shape and has not PPI flags the price the owner/dealer is asking seems to already very good. Late model 456's with low mileage can still go for quite a bit higher than 47k. The average across all of the 456 variations seems to be ~50k.
Some 456 owners may chime in here with some more specific information as to what to look out for.
What was your impression of the car? Did it handle well? Any funky noises? Windows/heat/radio/electricals work? Did you have a ridiculous smile on your face for an hour afterward?