In general, it's not possible for one app to interact with another one directly - for example, there is no way to ask Safari what webpages are currently open in each tab. It's also not possible to read or write Safari's bookmarks (though Pythonista's version of the webbrowser module provides limited access to the reading list), and Apple's Notes app has no API at all (as far as I know).
However, you can use Pythonista's share sheet extension to "share" a URL from Safari and run a Python script that does something with the URL. For example, your script could download the URL's contents and then process the HTML code to extract the text for example (the requests and bs4 modules are useful for that).
To get the processed text back out of Pythonista, you can use the share sheet again (which you can invoke from your script with the dialogs module). Some apps also have custom URL schemes to perform various actions, which you can invoke using the webbrowser module. Apple's apps usually don't have custom URL schemes (or at least not very useful ones). Pythonista also includes an evernote module, though I have never used it myself, so I don't know how exactly it works.