You're right, after re-reading the Power section on the datasheet it seems connecting 5V to the VREG_VIN should suffice to power the digital domains, but if you want to use the ADC, you still need a external 3.3V source.
> A separate, nominally 3.3 V, low noise supply (VREG_AVDD) is required for the regulator’s analogue control circuits.
It seems it would be painful trying to run this without 3.3 V.
The chip needs a) 1.1V to power the cores, b) 1.8V-3.3V to power IO, and c) 3.3V to properly operate USB and ADC.
The chip has one onboard voltage regulator, which can operate from 2.7V-5.5V. Usually it'll be used to output 1.1V for the cores, but it can be used to output anything from 0.55V to 3.3V. The regulator requires a 3.3V reference input to operate properly.
So yeah, you could feed the regulator with 4-5V, but you're still going to need an external 5V->3.3V converter to make the chip actually operate...
The TL;DR is that 3.3v must be fed into IOVDD for 5.5v tolerance to work.