Quote Function Missing Ability

That is correct. The base price is the price of the product itself, which works as the "base" for the configuration. It's basically the "bottom" price. If you need the bottom price to be zero, then set the BTO price to 0 and add a new item to the configuration to account for the price difference.

For example, take the "MailUp Subscription" product listed on our own software store. This is a Build To Order product. The price for the product is 0 as the actually price varies dynamically depending on the bandwidth purchased.

On the configuration page, though, you can see that the price starts at $50, based on the "default" items that have been added to the product configuration.

Setting the base price to $0 and driving the price entirely via the configurable items assigned to the BTO product can give you a great amount of flexibility, including when you are editing a submitted quote.