I would have to disagree with Burt just a bit...
It is really a toss up. If you are good with PHP, then make the core changes. If you are so so, then use STS.
By the way...Brian has not been around here for a while and no longer supports STS. The quote you took from his web site is for a much older version of STS. The modern version does allow you to template the infoboxes, home page, popup image, category pages, product pages, product content, etc. etc. etc.
STS is way more than a layout tool. Yes, it started out like that but has since grown in features and at the same time became a lot easier to install. It get along great with other contributions and does not slow your site down like the earlier versions of STS. It configures in the Admin much the same way your shipping and payment modules do. You no longer have to make any changes to your includes/configure.php and admin/includes/configure.php files.
It not anymore difficult to upgrade an osC shop with STS installed than it is with any other contribution installed. I do not know of any shop owners who use osC in the "out of the box" state.
:thumbsup: It is really up to you and what you want to get out of osC.
Just my less than two cents worth. :-"