To make it clear you want to have option to make partition active and install partition only to /boot sector? Well, I worry it won't work, you need to install bootloder to extended partition as usually code in MBR ( not sure about current status of windows, but old one do not recognize logic partitions ). About generic MBR I agree that if you manually uncheck it, it should keep unchecked, I have to check code there. Thanks for report