Fix to override namespace if set for k8s manifest

[knanao]

What this PR does / why we need it:
Currently, pipecd.dev/resource-key annotation is wrong because of this, which means every key will have been apiVersion:ResourceKind:default:appName if not having it in the manifest directly although the namespace is set in the app.config.yaml.

This will resolve the problem that k8s resources aren't pruned even if running Quick Sync

Which issue(s) this PR fixes:

Fixes #

Does this PR introduce a user-facing change?:

Fix the problem that k8s resources are not pruned even if running Quick Sync

[khanhtc1202]

Nice catch