I've ran both scenarios on my machines, and haven't run into any issues. I monitored the installation of UFT 12.01 over my 12.00, and it went through an uninstall of the older version that worked fine and replaced the files with version 12.01. It picks up the license and everything.
Some people recommend doing a clean uninstall of everything, and that's probably the most ideal situation, but if you don't have the time or patience to do a clean uninstall, I think you should be fine installing over the in-place version of UFT.
One thing I DID notice was that I had to manually remove the older Google Chrome extension when the install was finished, as it had two extensions. You want to leave the one that came from the Chrome Store and remove the older version if you run into this.