🐛 Fix reconcile order for new Shoots

[maboehm]

How to categorize this PR?
/kind bug

What this PR does / why we need it:
Fixes the bootstrapping of new shoots / when adding the extension to an existing shoot for the first time. Currently this results in the following error:

lastOperation:
    description: 'Error reconciling Extension: error reconciling secrets: failed to
      copy secret: namespaces "flux-system" not found'

Since the Secrets are always created in the flux namespace (usually flux-system), we need to do this after Flux was installed for the first time.

After flux was bootstrapped, we will still need to reconcile the secrets.