It doesnt matter how you do it. Just remember that once you do it one way either leaving the line or sanding it off do the same on all parts and they will all be the same.

I like to cut just shy of the line and sand until it just disappears. Plans are never perfect due to weather can cause the paper to shrink expand whatever. but if you stick with the same method of cutting out and sanding your parts they will all be only as good as the plans were no matter how good you are at cutting them all the same you will always have to touch them up when building.

Joe