What you have to look forward to is the rot will invariably spread. Rot is caused by a fungus infection (wood destroying organism), and it easily moves to new wood. Not only that, but Luan is not generally an exterior rated panel and would quickly deteriorate anyway. I would not be comfortable with using Luan in that application, and any rot needs to be removed back to solid wood, and treated.
This has a direct effect on the value of your home as you will not be able to pass the pest inspection without significant mandatory repairs if you want to sell. The workmanship you describe is not professional, and you may have recourse through your contract or contractor licensing bureau.