I got similar problem and solve it. My MetaXR plugin is for ue version 5.2.0, and my engine version is 5.2.1. When i try to package my project, AutomationTool cook all asset without shader in MetaXR plugin. Because the tool just don’t load plugin by default(the version no match).
It’s easy to solve it.Just set the ue version in .uplugin file, make it the same with engine version. Or you find a match plugin and replace it.