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It is actually NOT possible to delete pre-defined structure elements. You'll find that the "Delete" option remains greyed out, even though you remove protection. The reason for this is basically what @DeckOfManyThings outlined. If you ever choose to import shared material from someone else in the future, that content may reference to elements and needs to be able to find them correctly in your realm. So the proper approach is to simply hide them and then you'll never see them when working with your content.
Any changes you do make to the structure is LOCAL to the realm in which you make those changes. So you can run one game with everything enabled, another with only a small number of things enabled, and yet another with something in between.
Hope this helps!
P.S. If you experienced a problem with your realm, please post about it in another thread. If that problem was a crash or other nasty failure along those lines, please submit a bug report. There's a sticky thread with the details at the top of the forum.
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