OK, so I've been thinking about the odd choice for the microcontroller (amongst other things). And I have to conclude that there aren't that many Cortex M3 or M4 MCUs that would work from 5V. They clearly wanted to keep the compatibility with their ecosystem of boards. And after doing a search, you only get a few Cortex M4 parts with 5V, some NXP (expensive ones though), some Infineon parts (Insert vomit emoji) and some parts that come from the smaller makers.
If they would accept a cortex M0, then there is the SAM C21, probably much better choice,