I was under the impression that MakeMKV uses a temporary file, then builds the mkv file...not straight ripping in other words.
And considering BD Rebuilder, you can use the ripped disk as input, then output straight to mkv, compressed or not. If you want uncompressed mkv using BD Rebuilder, you'd have to adjust the settings in the alternate.txt file found in the Misc folder. It would be simpler to use a different tool though, like Blurip. BD Rebuilder isn't really set up for uncompressed output.
You can also work from the original disk if you have DVDFab Passkey or AnyDVD HD running in the background, but I don't like working from the optical disk...slows things down.