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This happens a ton when bootstrapping, but in my experience doesn’t really happen that much when modifying existing infrastructure which is typically when you care about it being purely GitOps a bit more. Argo has all sorts of flaws around bootstrapping things that isn’t necessarily Argo’s fault but they manifest themselves (har har) in weird ways. For instance I do a lot of crossplane these days and the fact that Argo doesn’t sync CRD’s and force them to exist before future sync waves is a huge pain point, especially when you start to get to more complex applications that have lots of resources. You find yourself having to manually sync CRD’s because the default ordering logic doesn’t wait for the CRD to exist before creating the downstream resource - even if you’ve specified sync waves!

A gitops repo can never be the reflection of the system's actual state. It's a desired state your humans want the system to reach eventually, sometimes defined very loosely. This is the idea since Weaveworks invented the term years ago. Unfortunately I admit it's not very intuitive, especially to engineers who are not super familiar with declarative systems.

You may have to use Kargo as well, also by the makers of Argo