I'm not sure why Flat File displays recycle bin data or why the process follows junctions, sym links, etc? Flat File has incredible use to find space hogging files without having to open or install another application.
I cannot think of a reason for these behaviors unless there's some underlying technical reason. I don't find the alternative of using Find and excluding these items a viable solution. I have drives that are 4T in size and Find is just too slow of an option. The caveat here would be if upgrading the Flat File process to exclude these items essentially makes it a clone of Find process then that's not a solution either.