No, there's no need to do things manually.
So, if you generate another application with the Maven archetype, you can customize it to some extent, without having to modify Portofino's source code.
Then, the issue becomes: are the modifications you want to do to the UI possible using only the extension points provided by the UI library, or do you have to build a new version of the library?
In the first case, you're done – just do your changes in the application generated with the archetype.
In the latter case, you're on new territory; you may want to follow the same approach as the demo-tt application, so have a Maven project with two modules, one the Portofino application and the other the modified UI. The Portofino application will then load the UI library from your filesystem rather than from the NPM registry.
Merely copying dist/ui does not work because dist/ui contains the standalone upstairs application, which is not the same as the Angular application that's generated by the archetype.
Hope this makes it clearer.
Alessio