My team is trying to solve the same problem and we haven't been able to identify a solution. Judging by the fact that an Esri rep has not responded to your question in over a year, I'm guessing that ArcGIS Pro does not officially support the use of docker containers due to the licensing issues that you mentioned. Containerization is an essential component within the modern GIS stack and it's frustrating that Esri won't recognize this and provide official support for it...