Well I don't know exactly how the Bluetooth in my comp works. I don't have a dongle, but I have built in Bluetooth. So I have nothing that would re-initialize the MS stack. I really want to try this (I just got Megaman X5 & X6 on my PC and I want to use the Pro Controller) I just don't want to screw up my laptops Bluetooth drivers or anything.For me, The toshiba stack only takes over 1 USB port. So even after uninstalling the MS stack and installing the Toshiba one, if I plug in my Bluetooth Dongle into a different USB port the Microsoft stack will re-initialize and take control of the device. Pretty handy. I can't say it will be like that for everyone but it is for me on Windows 7 64-bit using a Gigabyte Motherboard.
Edit: I am also on Windows 8 64bit if that makes a difference.