fails to flux bootstrap workload clusters

**What happened**:
created mgmt and workload clusters, flux bootstrapped to mgmt cluster without issue, however, flux did not bootstrap to workload cluster

**What you expected to happen**:
`flux-system` folder to be located in git repo under `clusters/w01` like it is for `mgmt` cluster

**How to reproduce it (as minimally and precisely as possible)**:
create `mgmt` cluster with a flux `clusterConfigPath` set to `clusters/mgmt`, then create a workload cluster with its `managementCluster` name set to `mgmt` and a flux `clusterConfigPath` set to `clusters/w01`

**Anything else we need to know?**:
`flux-system` folder is present locally inside `clusters/w01` under git folder

```
2022-09-28T06:57:14.659-0700 V3 Finished pushing cluster config and flux custom manifest files to git
2022-09-28T06:57:14.659-0700 V4 pulling from remote after Flux Bootstrap to ensure configuration files in local git repository are in sync {"remote": "origin", "branch": "master"}
2022-09-28T06:57:14.659-0700 V5 Retrier: {"timeout": "2562047h47m16.854775807s", "backoffFactor": null}
2022-09-28T06:57:14.659-0700 V3 Pulling from remote {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:15.894-0700 V3 Local repo already up-to-date {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:15.894-0700 V5 Error happened during retry {"error": "error pulling from repository: already up-to-date", "retries": 1}
2022-09-28T06:57:15.894-0700 V5 Sleeping before next retry {"time": "5s"}
2022-09-28T06:57:20.895-0700 V3 Pulling from remote {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:22.153-0700 V3 Local repo already up-to-date {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:22.153-0700 V5 Error happened during retry {"error": "error pulling from repository: already up-to-date", "retries": 2}
2022-09-28T06:57:22.153-0700 V5 Sleeping before next retry {"time": "5s"}
2022-09-28T06:57:27.153-0700 V3 Pulling from remote {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:28.399-0700 V3 Local repo already up-to-date {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:28.399-0700 V5 Error happened during retry {"error": "error pulling from repository: already up-to-date", "retries": 3}
2022-09-28T06:57:28.399-0700 V5 Sleeping before next retry {"time": "5s"}
2022-09-28T06:57:33.404-0700 V3 Pulling from remote {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:34.607-0700 V3 Local repo already up-to-date {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:34.607-0700 V5 Error happened during retry {"error": "error pulling from repository: already up-to-date", "retries": 4}
2022-09-28T06:57:34.607-0700 V5 Sleeping before next retry {"time": "5s"}
2022-09-28T06:57:39.608-0700 V3 Pulling from remote {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:40.864-0700 V3 Local repo already up-to-date {"repo": "darksystems/git/k8s-cluster", "remote": "origin"}
2022-09-28T06:57:40.864-0700 V5 Error happened during retry {"error": "error pulling from repository: already up-to-date", "retries": 5}
2022-09-28T06:57:40.864-0700 V5 Execution aborted by retry policy
2022-09-28T06:57:40.864-0700 V-2 error when pulling from remote repository after Flux Bootstrap; ensure local repository is up-to-date with remote (git pull) {"remote": "origin", "branch": "master", "error": "error pulling from repository: already up-to-date", "error": "error pulling from repository: already up-to-date"}
2022-09-28T06:57:40.864-0700 V4 Task finished {"task_name": "gitops-manager-install", "duration": "33.384918844s"}
2
```
**Environment**:
- EKS Anywhere Release: 0.11.3
- EKS Distro Release: 1.23

Start with the gitops-manager-install task and the Flux bootstrap flow described in the logs. Reproduce the setup using clusters/mgmt and clusters/w01 with EKS Anywhere 0.11.3, then trace the post-bootstrap repository pull handling. Done means the workload cluster bootstraps successfully and its flux-system folder appears under clusters/w01 in the remote repository.

Written by the indexing model from the issue text.