You are correct. When you pre order, you are simply paying for the item alone. Even if you were to be buying an item already available, this same system would apply. Initial payment is only for the item.
They will send you a link that will provide you 2 shipping options. Usually airmail tracking (cheaper) and EMS. Last time I ordered a single item for shipping, Airmail was NT$320 (about $11). My most recent order was for 2 items airmail shipping was NT$680 (around $23).
The site is very reliable. I've been ordering from them for years. My most recent order arrived a month ago no issues. They are also customs friendly and will mark your package as gift. In addition they also will hold and combine ship 2 items with different release dates.