When publishing a service from ArcGIS Pro 2.3 to Enterprise Portal (v 10.6.1 which incorporates categories) it appears that you cannot not assign categories to the preliminary published service. The adding of categories needs to be done separately when the service is a portal item.
When publishing a service from ArcGIS Pro add the ability to assign a content category from within the Sharing Pane. The content categories should include those that are in the Portal the ArcGIS Pro session is logged into.
I would assume that by logging into a Portal within ArcGIS Pro the software should be able to "pick-up" categories from that Portal.