Any disadvantages to single-supply mode?
The main reason would be for power efficiency. The voltage regulator inside the chip is a linear one, which means that its efficiency is: (VDDCORE/VDDIO). So if your VDDIO is 3.6v, then your efficiency might be only 33%! This is a terrible waste of energy, especially in a battery powered portable device where a long battery life is an important selling point for the device.

Poor power efficiency not only leads to a shorter battery life, it also generates heat. In this case it doesn't seem like much, but it can make all the difference. In a hot environment, that extra heat might push the chip over its specified operating conditions, leading to failure. In some applications, you might have lots of chips, which could create quite a lot of heat. In one application, we had 20 ET1200 chips, all using their internal regulators. Each chip's core uses just 75mA. But 20 chips means 1.5A on the cores, and a total of 1.2W of power dissipated just as wasted heat. The inside of the enclosure got pretty hot.