Once you've got a HTML/CSS website, what is the next language to implement into the environment? Provide examples of what the language would offer

JavaScript. And probably a server side language such as Python or php or ruby. Since HTML/ CSS are primarily just the structure and style of the site where JavaScript is your client side functionality and client side logic. And your server side language will be where be where your important business logic will be.

What are things that Python can do, that PHP can't?

Too broad, depends on what you are actually trying to do with your site. Do you need to implement rich client side functionality in a SPA? Start with Javascript and a framework like Angular.

As far as integrating with backend server functionality, you can do pretty much all the same things with every language you choose. If you want to keep the stack as consistent as possible front to back, use Node.js with MongoDb. Then all your code is basically JS and JSON.

Yes. Use the proper tools for the project. That said, php and MySQL are good to know

I agree with @Jumpshot44 since a majority of the web is run on php and MySQL.