In those days, it was probably 2. We now have a library that does the hard work for us.
At the beginning, I can imagine that porting that lib for the wii wasn't an easy job.
The library was already ported, otherwise we wouldn't have had access to the sd card.
The only extra thing that needed was to load the block list for the iso and use that to figure out where to load from when the game loads.
It had to do something similar for WBFS as well, because that can get fragmented too.
This had already been done on the PS2 USB loaders, although none of those were open source at the time so he couldn't just copy the code. However the documentation for them did say there was a limit to the number of fragments, so it was pretty obvious how it worked.
So because of one trivial bit of work he couldn't figure out how to do or even think it could be possible to do, we ended up with someone having to write a WBFS manager. Which would easily have taken longer to write than using FAT32 from the start.
This is quite common in software, that people will choose what they think is easier but is actually more work because they can't comprehend how to do it better with less work.
The alternative was that he knew how to do it, but thought that FAT32 would be a major problem that he needed to fix. I think there is enough evidence to prove that FAT32 is not a major problem & is easier to work with than WBFS.
Or he could have known it would be easier to use FAT32 and there wouldn't be any real problems, but wanted an ego boost.