If you authenticate an installer with your admin password, it has root privileges. It can do everything. Everything means that it can also set wrong permissions in case it's a faulty installer done by an inexperienced developer. It is rather easy to make a faulty installer if you need to install parts of the software at different locations (to be safe you'd have to make multiple packages and a meta-package and that's more effort).
"Repairing permissions" means restoring permissions to the factory defaults. It's not necessary to do this every week, but it might help if you experience odd problems. It's a low cost troubleshooting step, that's why it is suggested so often.