Files in /rw are persistent in an AppVM. (That is the reason why the configuration for bound directories is located inside /rw, if that wasn’t persistent it wouldn’t be very useful!)
From the docs you linked:
In an app qube all of the file system comes from the template except
/home,/usr/local, and/rw. This means that changes in the rest of the filesystem are lost when the app qube is shutdown. [Implicit: the changes in those three directories are persistent.] (docs)