Do you think that, in this example, using certbot is fucking shit up, or breaking something?

The thing about overkill is that it does work. If you're accustomed to using a solution in a professional setting, it's probably both overkill and also vastly more familiar than the bare minimum required for a class project that would be entirely unacceptable in a professional setting.

In OPs anecdote, they did get their certificates, so I don't quite see your "intentionally fucking things up" claim as what's happening.