I know this was covered on Battery University's site. With all the info there, it may take me a bit to find the exact articles to link here. In short, a high charge level doesn't mean over charged. It's above the point where extended periods can prematurely shorted a battery's life. Generally, this is 4.1V, which correlates to about a 75% charge level. All Li-ion battery chargers are designed to stop charging once full, so that has no bearing on this. Leaving a phone plugged in overnight is no different (chemically speaking about the battery) than fully charging the battery and removing it from the phone all together.
Saying frequent charging shortens its life is technically true but not in the way your article mentioned. Lithium batteries have a certain number of full charge cycles on them, but they aren't affected by short charges like older technologies. All things being equal, a lithium battery is affected by two half charge cycles the same as one full cycle. If you're a power user and doing multiple full charges a day, well then yes the battery will wear out quicker. Only that's a symptom of the heavy use, not how frequently it's plugged in.