“Problem” is one usually doesn’t start a design with editing pre-made stuff. A professional designer do this;
Paper > Photoshop > (x)html > main template (head, blocks, footer, general formatting) > more specific templating (content pages, lists, tables, forms, ie6 workarounds etc)
Creating something new by altering something that already exists isn’t the way to go if one want a good markup and all those custom things one is used to when designing websites. Just altering things is only the complete newbies approach that has little to no experience with xhtml/css in the first place.
The PHP-files in Wordpress isn’t really “php” in that sense since one hardly need to know any PHP in order to get it since it is mainly based on different hooks and the Wordpress Loop, well.. plus different custom fields and so on if one wants that. I’m not a PHP-dev in any sense (well, a little maybe) and i find WP’s hooks and everything extremely easy to grasp due to its logic.
I’ve checked the TPL-files but they are just too spread and it doesn’t feel necessary to have everything that wide spread in the template root really – everything that is a layout within a main layout (header, middle, footer) should be placed in an inc-directory. The important thing here is that a template should work with only those three files and then one should build from there by placing hooks or just simple includes <?php include ‘sidebar_right.tpl’; ?>.
There should be some sort of starter guide that just writes about the bare minimum in order to create a PrestaShop template and then lists further common hooks aswell as adding custom hooks. Problem now is that it feels way too much for that final step; custom main xhtml index > template files. I think you would rock your competition completely if you were the WP of E-commerce. 