I think that's a fallacy. Just because it works somewhere (and not great, as every bit of software has its own damn arbitrary format only it can parse) doesn't mean it works here.
It is conceptually a bit simpler, however that doesn't mean it is better.
after all I've only been administering linux/unix/windows boxes for 15 years so how would I know!
Installing by untaring a package, versioning the config files, adding comments...
I'd rather have a bespoke format than deeply nested keys in various locations (HKCU/HKLM/HKROOT and all that mess).
Having to find leftover keys, or to use pmon to find which ones are accessed is such a horrible experience.
I'm not sure why you are uninstalling software so often, nor why you are so anal about cleaning the entire registry.
But hey, it's a one click thing to deploy a registry change to a fleet of 10,000 AD boxes, one that can change the configuration of the 1Password app as well as MS Word, and have it done reliably.
Has never happened to me since perhaps the XP days.
Why are you uninstalling software so often through AD? Not that it absolves this issue, but it's not common to have huge software churn like this. And hey, isolate the issue and push a registry change to every single machine in the network, instantly and consistently.
It is conceptually a bit simpler, however that doesn't mean it is better.