I've done something similar with "caulk" along the seam, but only after the coating has been completed and allowed to cure for a few days. I didn't want to risk adhesion issues putting the sealant under or between layers of polyurethane, but IIRC some have put a sealant under polyurethane (directly on the fabric) with no issues.

Another idea is to use a squeeze bottle (like one might buy from the craft/hobby store for glue, or from a beauty supply for hair care products) to put drops of your poly coating right into the stitching holes after brushing on each deck coat.