This issue is no longer reproducible when publishing from ArcGIS Pro 3.6 to ArcGIS Enterprise 12.0. For older releases, registering the folder containing the .aprx file is the recommended workaround.
解决办法
Before publishing to ArcGIS Enterprise, add the UNC path of the folder in the script to the server data store.
Publish as a web tool. Ensure no data is copied, only referenced.
Run the web tool. The copied .aprx file contains the layer file in the Table of Contents.