On the B350 board, there is a quick switch between two of the SATA headers and the M.2 slot. So you will be able to run it as either x4 M.2 and up to two SATA devices or x2 M.2 and up to 4 SATA devices. The X370 board will be able to support x4 M.2 and up to 4 SATA devices all at once.
There are also different USB port numbers, but I don't think enough are exposed to begin with to make any difference. Someone was checking if the X370 boards x16 PCI-e slot could be bifurcated, but I haven't heard if Biostar got back to them with an answer; the B350 would not be able to be bifurcated.
Interesting point about the storage. I think the chipsets support different amount of usb, but the itx boards they are showing actually have the same (unless I misread). Kind of like the x370 supports sli, but on the itx board it doesnt really make a difference.
So it basically comes down to if you use a lot of drives you'll have to sacrifice m.2 speed.