How does a laptop PC actually calculate the remaining capacity of a Li-ion battery?

You are right. Battery voltage fluctuates over time, depending on the load. A hard drive spin-up for example, will load the battery for a few seconds, which will decrease the voltage by a few hundred millivolts. Furthermore, the voltage of the battery, as well as its actual capacity depends on temperature and other factors.

The best technique to estimate the remaining battery charge of a Lithium Ion battery is Coulomb Counting. The technique is based on measuring the current that is being drained from the battery in real time, for example once per second. The measurements can then be added up over time to obtain an estimate of mAh, milliAmp Hours consumed. The technique works the other way as well, to get an estimate of the charging progress.

With coulomb counting, it is necessary to reset the running total (the coulomb counter) when the battery is deemed empty, or set it to the maximum capacity value when the charging is complete. Charging completion can be determined by a process which is independent from coulomb counting. The 'resync' of the coulomb counter is necessary, because it is still just an estimate.. The battery capacity changes over time, as it wears out, as well as the termperature, and the load.

The best battery capacity estimation algorithms will have an ongoing 'learning' process, so that the actual capacity of the battery, the amount of milliAmp Hours that a fully charged battery stores is kept up-to-date.