That's why if you pay attention you'll often see your battery % go from 97%-100% and then back down to 97%. It is reporting as "charging" but in reality it goes idle to let the battery de-charge a little.
https://www.apple.com/batteries/maximizing-performance/
They don't say what "long-term" is, but monthly seems reasonable to me.
Also Apple seems to indicate that storage in a deep discharge state is far more damaging than storage at near-capacity based on the wording.
So if you're in doubt, charge it before you store it.
Finally, I don't think there's anything on that page that says you shouldn't keep your laptop plugged in when it's at 100%. I would be very surprised if they didn't have some cycle-conditioning going on. I have both a 2008 unibody and 2010 MBP, both essentially remaining plugged in for years. I don't think the battery life is abnormally low for their age, they still are capable of several hours of usage on battery.