I agree with Roman, somewhat. If you have items which can be enabled or disabled, then by all means leave those things in there. If they cannot be disabled, remove them simply because you don't want leave yourself open to the chance of having something improperly configured and someone accessing your other sites which are improperly configured.
That being said, it should be easy to go in and make changes to your site domain name, aliases and license keys. Yes, I'm sure there are other settings but they too can easily be added removed. One thing you could do is immediately before you perform your backup, is to add a site alias in for your domain so you can access it without going directly to the server and accessing it via localhost.
Lastly, there are scripts you could create or run which would update some tables but I'd highly recommend against this unless you know what affect it will have on your system and specifically what tables or views you need to query.
For the number of times this is performed in a year, it really shouldn't be an issue to go into the UI and make the changes. If you're doing it multiple times per year, you might question what the purpose of having DEV, QA, PROD instances. If you're simply looking to update content, then use content staging and post your content backwards.