There's critical difference between tags and category structure. With tags, each is independent and gets added to a list that is always alphabetized (unless you specifically order the tags, at which point you have to remove protection). With the category structure, any new section types and/or snippet types are added with positioning. Even if you just leave them at the end of the existing list, they are still added to the positioning information within the category definition. This positioning requires that you remove protection from the category, since you are fundamentally modifying the category, albeit in only a small way.
If all you do is ADD new stuff to a category, you are completely safe. Yes, you need to remove protection, but all the changes you're making are "safe", since they are purely additive. So adding the "Archetype" is perfectly fine. Hiding the "Class" is also perfectly fine, since you're simply hiding it and not actually deleting it.
The detailed explanation about removing protection strives to explain this. However, it seems that we could have probably done a better job with the explanation. If you have any suggestions on how we could re-phrase the text to make it clearer, please share them, as I'm certain you won't be the only user that gets confused by this detail.
Your gut reaction against cloning the topic is a good one. The best approach here is to add what you need to the existing category and hide what you don't want. To do that, you'll need to remove protection, but you should be fine.
Hope this helps!