I see two questions from your text:
1) Is PHP programming on Linux different from programming on PHP on Windows?
Answer: No, it is not. There may be other tools you work with, but even on Windows you have many options (from a simple Notepad to an IDE). There are many tools available on both platforms (such as IDEs such as NetBeans or Eclipse), which makes it easy to upgrade to Linux. If you want to run Script on your local computer, you can install the basic LAMP configuration (Linux Apache MySQL PHP) on your system, comparable, for example. XAMPP on Windows. Or you can install only php-cli (command line interface) without a full web server if you want to run only some scripts on the command line.
2) Is Linux difficult to use?
Answer: No, this is not so :-) The best way to find out is to get, for example, a distribution of Ubuntu that is very convenient for Linux and try it yourself. You can run the System as a Live CD without installing anything if you want to test something. After a bit of working with Linux, you quickly got used to it, and even application development should not be so difficult.
I can not recommend any books. Maybe someone else can.
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