It seem obvious to me that non-inverting buck boost for this particular application is a poor choice. The larger footprint and cost would make me chose the sync buck right off.
But what about using a inverting buck boost? If the source is a battery why not connect it up so that the micro gets the proper polarity voltage it needs? You could operate the inverting buck boost in transistion mode for high efficiency and the footprint would be the no larger than the syncbuck.
The other issue though is that the battery voltage really never goes low enough to warrant the boost in voltage.