It's more difficult for someone to steal their IR database.

But mainly, they can maintain a central database making sure that all customers have the same (and up to date) codes and configurations to choose from - this simplifies support tremendously.

It also means that they can easily make changes to customer remote configs remotely to help someone.

Beyond that, if you want a very good universal remote where you will be responsible for essentially programming it, including logic, then you can look at Universal Remote Control's (URC) Complete Control series. Expect price to start at USD $400 per handset when you buy from an authorized, but discounted, dealer Normal price would be around $650 for what such a dealer would sell for $400, un-programmed, or around $900+ fully configured for your home theater by a custom installer.