I lost a buccaneer's shirt because of this back in January (when full inventories were common) and the support in this game is non-existent. GMs do fuck all and contacting support via e-mail had me running around in circles. I eventually gave up trying to recover the item. In FFXI they have a feature where support will get items back for you in situations like this but as I say support is non-existent in this game. I can see this becoming a bigger issue further down the line.

The scary part is most of the player base are in full support of this game having no support and blaming the player when badly designed systems such as this go wrong. The game has checks for just about everything else where an inventory is full and has measures designed so that you don't lose the item but they did not implement any such feature for where it matters most; your hard earned runestones.

There's absolutely no reason why this item should not go into your loot list. Don't say it's because you could trade it because that's irrelevant when you can trade the item given for the runestone. There's also no reason why it can't be given back at the aetheryte, the fact it's a chest reward and not a leve reward is irrelevant. It simply boils down to another aspect of lazy coding by the old development team.