Why are my out of stock simple products treated as in stock in Improved Layered Navigation?
This is a peculiarity of Magento default indexing. It summarizes information on all the simple products and assigns it to the configurable products.
In case you have some configurable product with several out of stocks, they will still be managed by the navigation, e.g. blue color product (simple) is out of stock, yet if you select the blue filter, its configurable will be shown. Here is an official Magento report on this issue.