Good question! In the past I have basted top to bottom left to right, then a big x- corner to corner. Most of my quilts are hand quilted but I have used the same basting method & really haven't had any problem removing my basting threads. Sometimes I've had to cut close to the machine quilting then pull the basting threads out but the machine quilting I've done has all been 'in the ditch'.
Sorry this isn't more definitive.