I'm guessing that backup manager 1.1 will work on whatever firmware your dongle breaks. So if your usbbreak dongle only breaks 3.41 then It doesnt matter what backup manager you use. It will only work on 3.41.
To quote from the site: "We will be releasing our new and improved Backup Manager v1.1 on the 20th of October. As well, we would like to announce that our updates for newer firmwares will be delayed a few days."
As for if you have to do anything to the usb dongle, not sure about that, but just guessing that you wouldn't have to for the manager 1.1 . For the newer firmware support i think you might have to, but i guess it will be simple. So let's just wait