I don't understand what you mean about packaging code.
Do you mean to distinguish between setting up an EC2 instance or digitalocean droplet type of thing versus using ansible/chef/etc orchestration among the servers? Implying you would have to publish the configs for all your servers?
That would make no sense, both from a practical perspective (publicly disclose server configs? those can include sensitive information), and a theoretical perspective (what does that have to do with the source code at all?).
Problem is that unless you are installing your servers by hand you end up re-packaging wiki.js and then your own packaging code and the modification on wiki.js as a build artefact are now supposed to be public as well.