It means that as with all batteries, the usable capacity and lifetime are dependent on chemical reactions that have hundreds of variables, some of which aren't fully understood. Any estimate of battery capacity is just that - an estimate.
Measuring how much current can be drawn and what it does to the voltage as it's discharged gives one indication of capacity, as does seeing what the voltage does as it's charged at a constant current. But depending on how the charge is used, the cells may respond differently, so if the car's driven in a different manner (eg being in a hilly area for a few days) then the previous estimation won't necessarily be correct.
The BMU does its best to keep the cells in good condition and well balanced, but it doesn't always have the ideal conditions for doing so. This is true of any Lithium battery. Give two identical mobile phones to two people, one playing Candy Crush 12 hours a day and Snapchatting every 5 minutes and the other just making the occasional phone call once a month and after a year the reported battery capacity of each won't be the same. Yet the batteries started out near identical.
I'm not going to obsess about the battery reporting that it's got slightly less capacity than it had when new. Petrol engines also don't provide as much power as they once did as they wear over the years too. Only if it degrades to the point of affecting useful performance will I be concerned.