This is a common question we get asked, particularly from those of you who are building a WaaS or SaaS. There is no uniformity in terms of how different plugins and themes offer their licences, so currently they need to be managed and/or applied manually. That said, making the management of these licences easier for partners is very much on our radar, and we have a few potential solutions in mind.
If this feature is important to your business needs, we would love to hear more about your specific business and what your requirements are. The more the more information we have the better the feature we can deliver. It might even help to make it higher priority on our product road-map!