The point is that you may want to have more than one environment where PHP and Mysql are combined. At a minimum you probably want a Dev environment where you write the code and do initial tests, and a production environment where you put a copy of the code once your satisfied with it so that real users can connect to it.
Because PHP and MySQL are cross platform, your Dev and production environments don't have to run the same os. Your Dev environment could be a pc running Windows, and production could be a server running Linux.
However a few things work differently on different operating systems, so there are advantages to making Dev and Live use the same o.s. and generally be as similar as possible.