I don't agree. Those kinds of paths are often result of concatenation of several configuration options. Like APP_DIR=/some/app/bin; LOG_DIR="$APP_DIR/../logs". And APP_DIR comes to you from distro scripts, so you're not going to fork those scripts and support your own fork across updates, you just build upon those scripts.
The whole point of having an APP_DIR option is so that you can change it and things will just keep working. By doing $APP_DIR/.. you invalidate that by making assumptions about the parent structure. In particular something that could easily happen in the future is that you may not have write access to "$APP_DIR/.." You gotta do what you gotta do, but it is smelly.
If user gives your app a directory to play with, exiting that dir via ../something is the last thing you should do, it's horrible malpractice that just causes annoyance
"distro scripts" near always just show direct path to /var/lib/something for data and /usr/something for rest.