I make mine really snug when I make the join. Even an extra quarter inch is going to show up later. Another thing, your feed dogs are what pulls the material through. You can get puckers on the top if both parts don't pull through equally.
Question, are you sewing all but the final foot of binding down before you do the join? That only gives you 12 inches for any extra anything to show up. Easy to see if you are going to have any extra. FYI...I still hate that join. I always have to sew it several times. I'm very good at ripping!