/home was chosen because logstash will write things here (elasticsearch if run embedded, file input state)
Ultimately, it's all up to personal preference, and you'll find no agreement on that preference by anyone anywhere ;)

That said, why change the working directory to /opt instead of /home?

With this whole patch (#503), uninstalling logstash will no longer clean up after itself (You'll still have /opt/logstash littered with temporary and state-tracking files).