Wisdom of storing help files in user directory
Here are several cases where having documentation in the user home folder make sense:


Each user of the Xcode program has different bookmarks, needs, choices of what to download
Backup situations where only user files are preserved (common in corporate situations where they image and deploy apps systematically and therefore skip backing up files that come from the standard deployment process).
Networked home folders where you work from more than one Mac would cause another location to fail.


Gatekeeper and other code signing / security checking technology makes it poor form to store added content (or content that updates outside the normal app update process) in /Applications. /Users/Shared is not a good place to store things since it breaks under the network home folder use case. Thus ~ is left as the least bad place to store this content.