When specifying the managedOsImage you can apply flags in this way:

apiVersion: <http://elemental.cattle.io/v1beta1|elemental.cattle.io/v1beta1>
kind: ManagedOSImage
metadata:
  name: upgrade3
  namespace: fleet-default
spec:
  clusterTargets:
    - clusterName: my-cluster
  upgradeContainer:
    command:
      - "/usr/sbin/suc-upgrade"
    envs:
      - name: FORCE
        value: "true"
    image: myimage:mytag