The ls output shows that you have created the directory /home/usr/.app (and the files within it) as root. So neither the directory, nor the files in it, have write access for 'user'.

if you do to change ownership of the files, you'll find that 'user' now has access to them.

Yes, much better. That's the normal place to put application config information, and it goes on the same partition as /opt, so it doesn't use space on the root filesystem.