Oh wow, I never took into account how that scrolling input would be taken in something like Java, Flash, or Silverlight.
It's more of a general comment that the feature is horrible, and I think 99% of users are looking for the preference to turn the bloody thing off. But Java, Flash, Silverlight, etc, all allow for scrollable windows within their environment. I don't imagine the end result is any different than any other part of the OS, but Adobe is just trying to point out that this behavior is actually NOT their fault, but rather a system-wide thing.