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But no program should make any changes to a file I've created without my explicit permission.
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Then Sigil is not for you. It enforces its own structure which must be observed. But Kevin who is actually developing code can tell you more on this.
Especially in book view, it tries to guess what you want. When you delete or insert in book view, it guesses where you want to be, which might not correspond with what you think it should be, but for which there is good reason.And it tries to keep the epub valid, when you might not care if it is valid at the particular moment because it will be after you get done. Sigil is not so good with junk as input as it tries to make it right. Calibre editor doesn't care about whether it is valid at all. That is entirely the user's problem.
Keeping book view in line with code view is very hard, which is why calibre editor doesn't even attempt it.