Basically those “compilers” can do quite a few things. One is they can obfuscate the code which makes it extremely hard to read and or reverse engineer. Others may however convert it into byte code that can be utilized by the .NET framework, or the Java Virtual Machine for example.
There are also other situations like PHP GTK where they try to use the language to create desktop applications (I don’t remember if it needs compiling or not). Either way it seems that many try to push the language a little too far in my opinion ;p If your wanting to do stuff like that just go with Java or python, it’s much easier to work with. But that is sort of getting off topic.
I will add however another good IDE that I have used, not for PHP however but I do know it has an extension, is NetBeans. It’s mostly used for Java development, but it is an outstanding IDE and its free.