It does have to do with not ruining the battery. Lithium batteries dont require over charging due to memory like the old NiCads did. Once it hits 100% it stops charging and starts discharging. After it reaches a point it will charge again to full and repeat the cycle. Ive pulled batteries off after it hits 100% though and slap it in the phone only for it to say 97-98%.
As for not lasting long at 100%, since I turned off touch sounds and lock screen sounds it seems to last a bit longer than it did prior.