the opf file, all the html files are produced by Creator - as someone already pointed out - as an intermediate stage. At this point it would be possible to manually edit those files before building the finished .prc file.
E.g. I had an html file where Chapters were formatted using the <h2> tag. In Creator I could automagically have it create an TOC for me taking all <h2> headings from the html. Unluckily there were other parts also formatted as <h2> and so I took those out in the intermediate files and built the book afterwards.
Of course it might an easier way to edit the html file before importing it into Creator, that depends on how many changes are necessary.
Another thing I stumbled over and which might be useful information for people working with creator: Images in the html file (i.e. <img src=... ) are not copied to the working directory of Creator and are therefore not present in the intermediary files. The tag is converted just fine so if you manually copy the pictures to the directory where the other intermediary files are located then the pictures will apear in the .prc files as expected. Otherwise you get missing links to the images which might even crash the Cybook.