Read up on WebDirect especially what is supported and what is ot. Doing custom web publishing as you are doing is infinitely more customizable.
But can it be used for a limited website meaning is it for instance possible to have a url other than /fmi and will it found on google, can you see it without login etc, etc. I understand that there are limitations. Finally do you think FM will go that way.
No and no. You still need to login, even if it's the Guest login. I don't know if Google indexes such sites.
If you've already got PHP and mySQL running, why not drop filemaker??