If you create an organization folder, you can define an orphaned item strategy in its configuration screen, but this applies to the organization folder itself—in other words, whether and when its direct children (multibranch projects) may be deleted. All of the multibranch projects, which are unconfigurable, have a predefined new DefaultOrphanedItemStrategy(true, "0", "0"): delete obsolete branch projects immediately.
It would be useful to be able to define the policy to be applied at this lower level. Could for example be an additional selector for the children's policy.
Or at a minimum, the policy defined at the organization level should be assumed to carry over: disable deletion entirely if requested; if requested but using a nonzero daysToKeep, use the same value. (Not sure it makes sense to interpret organization-level numToKeep as that would be counting repositories, not branches, which might have entirely different typical values.)