I prefer to fold the end of the webbing when practical, but I do have a few packs that simply terminate in a bartack or seam without too much issue. If only a small amount of webbing is folded over it can be hard to insert the stay into the small pocket, but if you leave the end unstitched you will easily tell if you missed as the stay will pop out.
Between bartacking and ending the webbing in a seam I prefer the latter by far, in entering the seam the webbing usually turns a bit of a corner which means the bulk of the stress is transferred to the webbing rather then into the stitching.