I find this "code highlighting" very annoying. Can someone show me how to disable it on PHPStrom, and perhaps explain why this happens?
Here's an image of my Js/Jquery code on PHPStorm IDE:

In the WebStorm preferences go to Editor » Color & Fonts » General choose Injected language fragment from the list and turn off Background chackbox.
It's hard to answer _why it happens) - it's just a preference. Maybe someone prefers to see injected code (the code in language other than the main one used in given file) clearly marked. For me, it's also a distraction, I have just turned it off inspired by your question ;)
That's Language Injection in action.
You cannot disable it -- ATM language injections in JavaScript cannot be disabled.
But you can remove/change background color at Settings (Preferences on Mac) | Editor | Colors & Fonts | General.
Update: 2024-08-29
This feature has now moved to; Editor > Color Scheme > Language Defaults As of today, last option at the bottom called "Template language".
By switching this off, you can remove the mixed code background highlighting.