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Yes. Sigil currently demands full control of the directory structure within an epub archive. Any epub saved with Sigil will be altered to comply with those structural requirements. There is hope that that will change in the future, but it's not practical right now.
Calibre's editor will allow you to define your own internal structure if such a thing is important to you. Just don't make any edits with Sigil after you've created the internal structure you desire.
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