The info in the article is anecdotal. Lithium batteries have a finite life, and will lose capacity steadily as they are charged/ discharged over that life(usually 2-3 years of steady phone use).
They are very dangerous if not properly charged,(charging over 1C,voltage over 4.2 or even discharged well below 3 volts) and can ignite and burn just like an incendiary device.
If people were damaging the batteries by over charging them you would be having FIRES!! not low capacity. The charging circuits in the phone protect/prevent the batteries from high/ low voltage/ high current.
With all the junk cell phones are asked to do now,(load on the battery) no wonder people preceive the batteries as no good.