Using NDISwrapper is always a last resort as it will provide very limited control of the card. Also, as it always will use the Windows version of the drivers I am not sure that it would be the best idea to include them within a Linux distribution. The reason is that in case something does not work like it is supposed to it will be next to impossible to track down and fix the problem as the drivers most definitely are not open-source and not even meant to work in a Linux environment. This approach is only a workaround of the limitations of the current r8187 driver, until it will support WPA/WPA2 in managed mode.
Yes, as it will re-load the default driver for your card. As have been pointed out multiple times in this thread the approach described in the guide is only needed to actually connect to a WPA/WPA2 encrypted network using the Alfa card. For anything else you use the default r8187 driver that is installed by default and working flawlessly in BT3F.rmmod ndiswrapper
This allows me to use airmon, aireplay,dirodump ??