The battery monitor doesn't actually measure the amount of charge remaining. It measures the voltage currently provided by the battery and translates that voltage (which drops as the battery discharges) into a % remaining. To do this accurately, the iPad must have a reliable "profile" of the drain that occurs with the battery over time. That is why Apple recommends that the battery be fully drained once a month, or so. Doing so updates the "profile." (It has nothing to do with prolonging battery life.)
It's unclear why you might see a difference between the % remaining before and after rebooting, but I suspect that the iPad may reset the battery drain "profile" when you reboot. As the battery drains you'll probably see further corrections. Sometimes this means that the % remaining may appear to drop rapidly for no apparent reason. But that's probably just because the voltage reading and the profile of remaining battery have been updated.
All of this means, by the way, that trying to determine what is draining your battery at any particular time can be tricky. About the only way to get accurate data is to engage in several days of testing with careful variation in use of various apps, notifications turned on/off, etc.