Even if you are the only person using your Mac, there are still two 'sections of the hard drive/computer: Yours and the OSs. You can put anything you want in your own section but the OS is allowed to put anything it wants in its. Now, should you ever want to create another 'identity' on your machine, you might not want them to have use of everything in your folders ( and vice versa ). That's where the "Home" thing comes in, it's actually your "Users" area, every 'identity' created on your computer will have their own 'user area'.
However, if you have a few applications that everyone might need to use, you can allow that easily by placing that application in the OSs section. Now, everyone can use that application but they can save the files/documents in their own, private 'user area'.
You will often see an application installer ask if you want the app to be usable by everyone using your Mac or just you. That's its way of deciding where to install the actual app, in the OSs area, or in your 'user area'.
So, you can generally, put every app in the 'main' Applications folder and never be bothered by the one in your 'user area'/home folder. But if you ever need to create a space for a limited purpose user ( a children's identity for playing games, for example ) you might want to have a more secure set up; that's the real intent of these 'identities' and double Applications ( and many other directories ), anyway.
It's a feature, not a bug!
