On a pattern ship where the slight lift and weight difference will make an airplane not track through loops consistently then it can be worth correcting regardless of the building stage. Nothing is worse than having to correct for loop tracking. Contests are scarey enough without having a badly aligned airplane to make it worse.

On a trainer a 1/2 inch is not a big thing and having one aileron a little longer than the other will not effect rolls and similar maneuvers. However the differential span will still mess with loops a little. If you are still in the balsa stage, change it to be correct, it is just a good habit to get into. If you get enough little accidents adding up the wrong way then it can mess up the handling of the airplane. If it is covered and ready to fly don't change anything unless you or an experienced pilot notice something that could be a result of the inbalance.