I have the following declarative pipeline:

pipeline {
    agent { 
        kubernetes {
            defaultContainer 'jnlp'
            inheritFrom 'mypod'
            yaml libraryResource("my-template.yaml")
        }
    }
...
}

where my-template.yaml only adds tolerations and affinity rules to the pod.

The resulting pod template includes the tolerations, but not the affinity rules...