Simple question.
Do browsers cache PHP generated CSS and script files automatically, just like CSS/JS files?
If the URL remains the same, and there aren't hints in the HTTP responses to tell the browser otherwise, they can be cached.
If the URL includes dynamic information, the browser probably won't be able to take advantage of caching.
Changing the URL by adding a timestamp as a dummy parameter (e.g. http://host/myfile.php?t=17279273) is one of the ways you can prevent caching since the browser sees the slight change as a new resource.
Sure, barring explicit acts to prevent caching. The browser has no way of knowing if the file was a static or dynamically generated resource.
Jonathon's answer suggesting the addition of a timestamp to prevent caching is a good one.
A useful tip along these lines is to append the creation/last modified date of a file. Doing this means that while unchanged the browser will cache the file, but when you update the file those changes are forced to your users.
It's not always the best option, but worth noting.