I'd like the input from an expert like Thomas or Toni Wilen, but repeatedly I have used WinUAE folders and FAT partitions on my Amiga without problems, extracting stuff with WinRAR. It works every time. Rarely I run into issues and usually it's related to filename problems (Amiga filesystems allow certain chars that Windows does not, like *)
It is often the case that I take a WHDLoad game, extract it on my PC using WinRAR to my FAT formatted SD card, then pop that into my Amiga and it works. No file attributes are changed that I can tell but I'll make a test right now.