Depending on what battery protection modes are in play, many have smart charging or other features designed to prolong life. Also a fair few batteries come out with greater than design capacity from the factory. It's called a design capacity and not an absolute capacity for a reason. A phone battery that left the factory at 110% could conceivably still be at or above 100%.
Fyi it's not overnight charging that's the issue either, it's charging to 100%. What one device consider 100% varies and devices will essentially lie to you about it. 4.2V is normally considered 100% full for Lithium Cobalt Oxide batteries yet some devices push higher than this while others skirt under to pad capacity and cycle life respectively. It's about tradeoffs.