I noticed that when deploying even using the parameter --to, it deploys to the domain set to .nsdeploy. Is there a workaround on this or should I always the domain in the nsdeploy?

Ideally it should ask you the domain you want to deploy to, when you use the --to parameter.

Usually all your deploy stuff goes under SuiteScripts -> Deploy_Extensions so I don't find any use of domain during deploy followed by activation. Only matters when deploying core or fetching active theme(s) and extension(s).