Typically I do put classes that do not touch database records in a different folder. However, the organizational bit really depends on the team that is developing the app. We very well could have put the twitter and printer classes in a "services", "business_domain", or similar kind of folder.
It's still pretty much true on my setup. The only difference now is Settings Sync is a build in feature and I also use the Remote - SSH and Remote - Containers extensions.
I have a bad habit of not being consistent. It's something that doesn't bother me as far as styling goes and I think I may have even turned off that Rubocop warning.
Honestly, the template if very bare. It uses esbuild/css-bundling (see the README) and installs bootstrap with a very simple layout with a navigation bar. That's really all the template does.