Puckers come from the backing not beinf smoothed out. I use my glass topped dining table and use clamps from Home Depot to hold the sandwich together. Smoothing every time I have to move it to a new section of the quilt. I can still get a small pucker or two if I unpin a too large of an area when quilting.
I leave the puckers, wash and dry it and they don't show as much. I always use high loft poly batting, never had a quilt coming apart yet. I have made over 110 quilts.
All that being said I would leave it and move on.