Just came across this thread while trying to solve the same issue. I have my CI/CD pipeline working now (for me Azure Pipelines but it shouldn't matter) so I thought I'd share.
The end of this article https://docs.nopcommerce.com/en/developer/tutorials/azure-deploy.html says to add extra build tasks for each plugin before the main build. I tried adding all my plugin builds separately but ended up just running my msbuild task twice. First time with args /t:build and second time with package parameters.
When building the solution the target output from the plugins arrives in Nop.Web/plugins too late and they are not picked up in time for the package operation. Building twice ensures that all referenced plugins that the solution references make it into the temporary build location before being packaged.
Hope that helps.