There are some major differences. I've owned both, and my current set of tools include a Rupes LHR21, LHR12 and a 75E. My initial opinion was that the 3401 is the better/more versatile machine, but over time, the LHR21 really is the better machine.
The Rupes 21mm large-throw DA has 21mm of throw versus the 8mm of the Flex 3401. More often than not, this allows for faster cut and and the larger throw also does a much better job of "flinging away" the abraded paint residue, which results in a better finish. And as you know, paint residue management is really the underlying key to most correction and finishing issues.
The Rupes can also use MF pads most effectively. MF pads generally do faster/better leveling than cutting foam. You can use 205 and the Meguiars MF discs to do some crazy things that you absolutely cannot due with a 3401.
And sure, the Rupes is not forced-rotation, but that is really a non-issue once you make some adjustments to how you attack your panels. Many of the complainers have not learned how to use the machine properly, and besides, pressure should really be one of the last things on your list of techniques to try.
A lot of the very curved surfaces that people are having issues with, are curved areas that should be handled by a smaller polisher like a 75E anyway.
So that's my opinion - skip the 3401, and get a Rupes 21.