Maybe you can look at an alternate quilt design for the other blocks. They don't have to be all the same. You have now learned that seam allowances is one of the things to take into consideration when you do choose a quilting pattern for hand quilting.
But stab stitching is about the only way I have figured out how to deal with those bulky seams. I think from your description you are crossing the seams at an angle. Just don't try to quilt parallel to the seam on the side that the seam allowance is turned.