We have scenarios when we share differently Map Image Layer and Feature Layer items (these items are created for one AGS map service - AGS is federated with Portal). For example, Feature layer is shared for a specific group (for editing, ..) within the Portal, but Map Image Layer is shared publicly. But when a service needs to be overwrite, ArcGIS Pro will override the items sharing according to the publication settings for both items. There is no option to control sharing for each item separately.
I suggest adding the ability to control sharing for all items at the ArcGIS Pro level.