Currently we are using ${HOME}/bin/kustomize edit set nameprefix prefix1
But it is adding nameprefix to all of our resources like deployment.yaml and service.yaml.
We want to apply nameprefix to deployment.yaml only and not apply it to service.yaml
There is github issue about that
And there are 2 examples provided by @jbrette with which you can achieve what you need.
Additionally you can take a look at these pull requests: