When you get a calibrated pair, they are made at the same time. After they are made, the resistance is measured and the card written with the details. Because they are made at the same time, subtle tweaks can be incorporated (for example, compensating for one covered and one uncovered pickup). This can't be done if you buy them at different times.
From speaking with Tim lots of times, this is done if you buy two different pickups as a set at the same time (in this case there may still be a difference between the pickup characteristics, but it is not as extreme as if you bought them separately). Also, and this is the important bit, you will get a bridge and neck pickup. In many sets these are totally different pickups (sometimes different magnets, sometimes different DC readings, sometimes even different wire). Sometimes the difference will be very obvious (Tom used to have a Miracle Man bridge with a Stormy Monday neck in his Foster LP), however they will work together. I have many mixed pickup sets which Tim set up for me (Emerald/Mule, Riff Raff/Stormy Monday, Nailbomb/Cold Sweat, Warpig/MQ, etc), all of them work together and in some cases, the neck pickups were wound specifically for the set.