It's just for calibrating the battery.
Let me just get this out of the way: most of the time it doesn't make a difference.
The only time it could (not always) make a difference is one of the following scenarios:
-phone sat for a long time while turned off (i.e before you purchase it)
-you hooked up your phone to the charger many times throughout one day and didn't allow it to hit 98-100% before you unplugged.
The battery has a chip built in [most lithium ion batteries have this because they are A) explosive and B) can kill you] which is responsable for a few things:
-"guessing" your current battery percentage based on the minimum and maximum recorded voltage value. For example let's assume a phone with a 5v battery shuts off at 3v. When that battery reaches 4v it will display 50% battery left.
-deciding what the shutoff voltage is. What I mean by this is let's say for example when your 5v battery reaches 3v at the end of the day, the chip decides it's time to shut off the phone and prompt you to charge it back to 5v
-constantly reading the the voltage in order to use that data to perform the decisions listed above
The voltage sensors in phones are, well, pretty bad due to the inherent space and power limitations. The voltage values swing back and forth between different values that are (sometimes) close to the actual value the battery is at. So the battery chip has to calculate an average based on all these voltage values. It then uses that data to do it's job, which is shutting down your phone when it needs to as well as display battery percentage.
So by leaving the phone in for a little longer after 100% once in a while, all you're doing is allowing the battery chip to collect more voltage readings in order to calculate the average more accurately. You're just doing it for the sake of sample size.
Realistically unless your battery is not calibrated, it doesn't really make a difference. But a phone that just came out of a sealed box is likely to need calibration depending on the manufacture date, or how long it "sat" for.
Moto X [Rogers XT1058]
Stock 4.4.2, Rooted and heavily debloated
Moto X Debloat guide
2x S2 i9100, iphone 4s, S3 I747, iphone 5, Nexus 4, HTC One