Lots and lots and lots of programs install in AppData. I consider it good manners for a program to offer the option.
You will find those programs
also (usually) offer the option to do an administrative install into C:\Program Files\
Would you believe that Chrome/Firefox offering AppData installs was actually considered to be an important feature? By developers
and users?
At least one place where this is a good idea -- how else do people install a decent browser on a corporate PC?
http://PortableApps.com -- useful as a last resort, but often overkill.
...
Checking my WINE install, Kindle for PC is installed in the pseudo-Program Files folder, not the pseudo-AppData folder.
What are the chances that you inadvertently told Kindle for PC to install locally rather than globally?