I suggest you could make a C2 theme framework for wordpress. I'm not sure every php files are included in index.php inside of HTML5 canvas.
Otherwise, index.php should be included one element like canvas with headers. Then in .capx it could include loop.php via AJAX and set text to read posts, then export to HTML5 and edit index.html to index.php with original wordpress index.php file.
I recommend you to test php echo inside of canvas before to develop a theme.