The 50% rule is confusing, but in my opinion it is not 50% of the Y fare, but 50% of the regular fare for whatever booking class you're booked in. The same 50% restriction applies to earning miles and flights and I accidentally ran up against it on a Y flight that was discounted 70% off the Y fare so didn't earn any miles. But I regularly fly in lower booking classes that are well below 50% of the full Y fare and always earn miles in them. So if you're booked into E for example, then you're only concerned if the price is less than 50% of the full E fare. They sometimes have special fares within a particular booking class and that is when this rule kicks in, but it's not often, at least on the routes I fly, other than domestic routes. I've never seen these fares on international routes personally but have heard from others that they do sometimes exist.