I think the intent of not allowing partially full larger bottles is to not have the TSA people having to try to decide whether or not you have 3 ounces or 4 in your 8 ounce container - but an empty container is empty, so no decision is necessary.

I am now thinking about whether or not I can get a stainless steel thermos through or not..... empty it will still look suspicious. I would guess that it will be searched and it will be wise to just put it in the box at the beginning, but I don't think it is a "banned" item...