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As DNSB has noted: new epubs already DO use the Sigil Norm structure as the default (unless you change it with your own default structure). Sigil just no longer automatically restructures ALL epubs upon opening.
As for the rest of your requests: we'll look into them, but it's probably too late for any of them to make it into the upcoming release. We need time for testing changes thoroughly before releasing.
RE the Regex Rename: I actually prefer seeing the filenames that aren't going to be affected. It helps to confirm that I've not made a boneheaded mistake before committing.
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