Am I maybe misunderstanding something? When I call https://freetz.github.io/wiki/, I get a 404 page even though https://freetz.github.io/wiki/index.html exists and works as expected. My interpretation of the 404 error message is that my provided index.html in the wiki/ subdirectory ought to be used automatically if it exists. But it is not used. Does this only work in the site's root directory?
I just ran across this issue myself. Do you have a readme.html or readme.md file in the same directory? If so, remove it and see if that fixes your issue. It seems that GitHub prioritizes readme over index.