The AM355x already has 2 x 32bit Programmable Realtime Units (PRU) [1] so the AVR seems a bit redundant (other than compatibility with existing shields and ease of programming)
Compatiblity with existing libraries and example code for other Arduinos is the key here. I find it surprising too, but there are people who do not really want to know all the low-level details but get the result quickly :)
Yeah, I don't see the point of the on-board AVR at all. It can't be just a voltage thing, because I'm sure they already have an ARM-only Arduino with shield headers.