If you are using the likes of AnyDVD,DVD Decrypter,DVD Shrink,DVD20ne, Nero, RNM etc., then you shouldn't find any limitations with FAT32. It certainly will not affect your ability to burn.
Nearly all of the easy click methods use files .... and these are normally only 1,048,574KB each, so when ripping, compressing and burning files, you will not get anywhere near the maximum filesize limit of 4gb.
If you intend to start authoring disks, with menus/creating images etc. and getting into more advanced things then it's possible that you will hit the size limitation.