Google's spiders essentially see what your web browser sees. If you want to see what a dynamically assembled page "looks" like to Google, just do a "view source" in your browser.
Doesn't matter if it was coded by hand or assembled using PHP and MySQL. It's all HTML by the time it gets to the web.
The SEO problems with CMS's arise when (for instance) they're set up to force the same title tag on every page, or where they don't allow the page to have a different H1 and title element, or where they don't allow the inclusion of alt elements on images, that sort of thing. The issues have to do with what data is in the database and how it gets pulled.
Once the page is rendered for the browsers and search spiders, though, there's no difference between the code of one that was dynamically generated from a database and one that was lovingly coded by hand in Windows Notepad.