I'm currently working on a long term project and ran into this exact issue. We're implementing the HR onboarding module and like you said, since this isn't in prod it's hard to exclude the data from the clone. I just actually enabled the module in prod and moved everything but disabled the creation of onboarding cases so when we clone I'll still have my work saved. 

I do like the idea of backing up the update sets/etc. But sometimes, things do not get captured and theres a good chance you will miss something. 

In this project I was working in 3 different scopes, so I had update sets everywhere and just didn't feel comfortable using the backup method.