The Spine Runtimes don't render bones per se, but attachments which get their transformation from their parent bone. A bone can either be always active (it's not in any skin) or only active if the skin(s) it is contained in is also active. Only bones that are associated with a skin that is not active will not be updated when the transformations are calculated. This however doesn't have anything to do with rendering per se.
I'm not the local Unity expert, but I can't seem to find a way for SkeletonUtility
to interfere with the above mechanism, as it doesn't concern itself with skins and skin bones (bones that are associated with one or more skin).
Could you expand on your problem description a little bit more? E.g. what do you expect to see and what do you actually see in your project?