Reason why applications aren't stored in the Home-Folder?
Apple's design is not at all a traditional or typical UNIX layout for user files, user preferences or application files and preferences so I would say this is just Apple.

They do document exactly how developers are supposed to design OS X apps to take advantage of the "canonical" locations where files and preferences should be stored so that each user can decide to install any application in one or several locations.


/Applications
/Another volume/Aplications
~/Applications
or anywhere else on the drive since on OS X - you don't need to place an application anywhere as long as the user can read from the folder - an app should run and store things in the proper pace (which is NOT in the application folder itself).


Here are three articles I would start with to learn more:


OS X File System Programming Guide
OS X File System Details
Apple OS File System Overview (iOS and OS X combined) Start Here and skip past the iOS part and go directly to Table 1-2 for OS X summary of important folders.