I'm working on the same problem. I also don't know what the root cause of the issue is, but have an idea for why you are still seeing some stragglers after your code change. As your fix is in the init() method, it only applies to quotes as they are created. Therefore, any quote that was created beforehand would still have this issue.

Run this query to get the quote_id of all outstanding quotes with more than 2 addresses associated to it.

I'm working on the same problem. I also don't know what the root cause of the issue is, but have an idea for why you are still seeing some stragglers after your code change.

The init() method is called in the CartController::indexAction(). So it only runs when the customer loads the cart page. If you have some kind mini-cart widget on your site--anything that shows the current subtotal but isn't the full-on cart page--then the subtotal will still be double in the mini-cart whenever there are duplicate addresses. If that's the case, it should be fixed as soon as the customer goes to the cart page.