You need to separate several concepts, programming, language and runtime environment.
Programming is the translation of a solution to a problem into a technical language. That is a somewhat generic skill, a good programmer will not particularly care about the language they are using. Programming involves repeatedly breaking a problem down into smaller and smaller problems until you arrive at a problem the environment has a built in solution for.
Learning Python should equip you with the ability to learn how to do the decomposition of problems.
The language provides some of the built in solutions to decompose problems into. The style of the language has a great deal of influence on how you'll probably break a problem down. Terms like 'object oriented' are ways of tackling problems, you can do it in any programming language, but in some languages the style flows naturally while in others you have to work hard to do it.
Python is not a language I use or know well, however my belief is that it provides a reasonable basis for learning programming.
The runtime environment of a language also provides solutions to decompose problems into. Sometimes those solutions provide actual limits on to what you can do, provides an environment that allows you to describe an operating system's most fundamental function, Python does not.
Python tends to be provided with a runtime environment that is more server application oriented.
So if you know Python you can write programs, normally the sort of programs that run on server computers rather than those that run on client computers.
Python cannot really replace Java. Java provides features that make it appropriate for writing business class applications and for more comfortably running on client machines.
Python is not really suitable for games and mods. Lightweight games tend to be written in Java or C#, heavyweight games in C++. Modifying games normally needs to be in the language they were written in.
But, yes, Python could technically replace PHP. That said, PHP is normally very appropriate in the places it is used.