I recently ran into a case where I was trying to reduce a .bc file and the interestingness test I had written reported that the input was interesting when run in isolation but when running llvm-reduce it failed the initial sanity check before reduction starts. Turns out that internally llvm-reduce only deals with .ll files and does not set the ShouldPreserveUseListOrder option when producing these. For this rare case setting the option made the difference between being able to reduce or not.
I suggest that we either always set that option or alternatively add a command line option to have it set.