I know I can do this manually, but it would be nice to have an option to leave the current program files alone and upgrade the configuration. Program file changes, even for someone who installs all the Beta upgrades, are a lot less frequent (in my case) than configuration tweaks.
On a slow USB stick or slow USB port, the per-file overhead is the main bottleneck in my experience, making the config the slow part to copy and the program fairly negligible in comparison. On a fast USB 3 stick and port it's all done in a few seconds. (Just from my machine, so maybe factors like antivirus scanning the binaries or diff speed devices come into play.)