Doesn't sound like the page is being cloaked... not if you were able to see all those links, etc. Sounds more like they just wanted to use some PHP to do something dynamic on the page, or possibly to generate headers/footers for the page.
The php includes will probably just be for ease of maintenance. I do that myself - all my pages are .html, but I use php includes and have my server set to parse html pages for php, for including some things like common tables of links. He could also be randomizing links via the php includes and then inserting them into the .html pages.