Q: Isn't FAT limited to 4GB file size but a game iso is larger than 4GB?
A: Yes, that's why the .wbfs files are scrubbed to save space and if it is still larger than 4GB it is split to 4GB chunks. Split files are named gameid.wbfs, gameid.wbf1, gameid.wbf2,... similar to how the a .rar archive can be split to multiple files (.rar, .r01, .r02,...)
Q: What about the file size, games on WBFS partition are scrubbed / compressed, will it take more space on a FAT/NTFS partition?
A: No, it will take the same space because the files are not in .iso format but instead .wbfs format, which uses the same scrubbing / compression method as on a WBFS partition, actually the file format is the same as the format of the WBFS partition. And to be even more accurate, the .wbfs files will take even less space, because the wbfs block size will be smaller too. (The size depends also on the selection which partitions are copied - all or only game)
Q: Is there any advantage using FAT/NTFS rather than a WBFS partition?
A: Depends on personal preference. These are some of the points:
advantages:
- no need to repartition in case the disk is already used for other stuff
- the game files can be copied using normal file managers
- the partition space can be shared for other purposes
- better choice of file-system recovery / de-fragmentation tools
disadvantages:
- limited choice of loaders: only CFG, GX and WiiFlow support FAT/NTFS at the moment.
- loading speed should be approximately the same compared to WBFS