I am not an argocd expert, so maybe I am missing something.
But it should support the app of apps patterns, at least up to a certain level.

The way Updatecli autodiscovery works is, it looks recursively for all files matching specific patterns.
Then for each identified files, it generates Updatecli manifest on the go and apply them right away.

Running updatecli diff should show you what updates it can detect. And running updatecli manifest show will show you the generated manifests.

Autodiscovery focus on a standard/generic update scenarios and then you may need to write manifest to handle your specific cases.
If you think that a "standard" scenario is missing in the argocd autodiscovery plugin.
Then You can open an issue and/or make a contribution.
The argocd plugin is defined on https://github.com/updatecli/updatecli/blob/main/pkg/plugins/autodiscovery/argocd

Worth mentioning, running updatecli diff is handy to quickly see what would be changed but if you want to automate the process of opening pullrquest then you need a bit more configuration as explained on https://www.updatecli.io/docs/guides/dockerfile/