I am not able to reproduce the issue. Here's what I am trying:
quarkus create app hello-quarkus -x kubernetes
I copy and paste the properties from your post and then run
./mvnw clean install
I check the generated files under target/kubernetes/kubernetes.yaml|json and I am seeing:
- name: JAVA_TOOL_OPTIONS
value: "-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=*:5005"