I attempted to install a BM SNO with the agent based installer.
In the install_config, I disabled all supported capabilities except marketplace. Install_config snippet: 

capabilities:
  baselineCapabilitySet: None
  additionalEnabledCapabilities:
  - marketplace

The system installed fine but the capabilities config was not passed down to the cluster. 

clusterversion: 
status:
    availableUpdates: null
    capabilities:
      enabledCapabilities:
      - CSISnapshot
      - Console
      - Insights
      - Storage
      - baremetal
      - marketplace
      - openshift-samples
      knownCapabilities:
      - CSISnapshot
      - Console
      - Insights
      - Storage
      - baremetal
      - marketplace
      - openshift-samples

oc -n kube-system get configmap cluster-config-v1 -o yaml
apiVersion: v1
data:
  install-config: |
    additionalTrustBundlePolicy: Proxyonly
    apiVersion: v1
    baseDomain: ptp.lab.eng.bos.redhat.com
    bootstrapInPlace:
      installationDisk: /dev/disk/by-id/wwn-0x62cea7f04d10350026c6f2ec315557a0
    compute:
    - architecture: amd64
      hyperthreading: Enabled
      name: worker
      platform: {}
      replicas: 0
    controlPlane:
      architecture: amd64
      hyperthreading: Enabled
      name: master
      platform: {}
      replicas: 1
    metadata:
      creationTimestamp: null
      name: cnfde8
    networking:
      clusterNetwork:
      - cidr: 10.128.0.0/14
        hostPrefix: 23
      machineNetwork:
      - cidr: 10.16.231.0/24
      networkType: OVNKubernetes
      serviceNetwork:
      - 172.30.0.0/16
    platform:
      none: {}
    publish: External
    pullSecret: ""

4.12.0-rc.5

100%

1. Install SNO with agent based installer as described above
2.
3.

Capabilities installed  

Capabilities not installed