Looking at your images as an example:
In the first one, you had to manually type in "New Bounty to Offer" using HTML code.
In the second image, in the same section, the title is replaced with this PHP code:
<?php echo WA_getCMSContent($database_PowerStoreConnection, $PowerStoreConnection, 'Home Page' , 'Popular Pod Title'); ?>
This allows it to pull information from the database instead of manually updating the page. That's the purpose of adding PHP code to your website. You can automate your site to pull information as needed instead of constantly rewriting pages. This is done to make the site more effective. The installation process just checks to make sure you have everything in place before trying to run the code.