Java Packages – Java-Style Package Naming and Second-Level Country Domains

The reason to have your reverse domain name as the beginning of a package name is to reduce the possibility of naming conflicts. This is especially important if you are writing a library or a framework. So that explains why "com" and "org" are in there.

Other then that, everyone is different and chooses their package structure differently. One reason option 1 might be better is if there is no real destinction between features or they have a lot of code that crosses over. With that, option 2 might make more sense if features really are mutually exclusive in some manner.

Also, I bet option 1 is generally the way most projects start, and then nobody ever changes it (or cares to) after. I wouldn't be surprised if a lot of companys don't put a lot of thought into their package structure anyway.

Global uniqueness. If everyone, or at least serious developers who distribute their code beyond in-house projects, adheres to that convention, it will never happen that you get name clashes when you add another third-party library to your project. Bear in mind that Java was initially propagated as a solution for code deployment anywhere, anytime (via applets and remote classloading over the internet).