I believe "packet boundary" just means that the host shouldn't fill out an otherwise short packet (transaction) with the start of a new CBW or CSW. In other words, make the previous packet a short packet if necessary and start a new packet with the CBW or CSW.
The bulk only spec defines the starting locations for the field in a CBW or CSW.
So as I see it, "Fields appear aligned to byte offsets equal to a multiple of their byte size." is just describing the structures specified for the CBW and CSW.