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@Dyspeptica - I'm assume you posted here just because your earlier comments were here but none of that has anything to do with this plugin, it is all ebook-convert command line and the Modify ePub plugin. But I will answer here anyways.
If you insert a cover during an ebook-convert operation, then Modify ePub can replace it with either of "Insert/replace cover" or "Update metadata" options.
If you don't supply a cover during an ebook-convert operation, but allow calibre to generate a default one, the same as above applies.
If you don't supply a cover during an ebook-convert operation, and tell calibre not to generate a default one, then there is no "blank background/generic cover" created by calibre. That page is part of your original ebook or a byproduct of the conversion pipeline for it, it is not a "cover" as such. To then add a cover, you must use the "Insert/replace cover" option of Modify ePub. Which will as you found add a new cover page to the front of your book since your book does not have a real cover already, leaving the existing content alone.
Using the "Remove cover" option of Modify ePub is an option you would only choose if it was your intent to strip covers from your books without putting any back in. It is automatically called behind the scenes when you choose "Insert/replace cover", so there is no point in running it in isolation - in fact it could be detrimental to do so. There are a few posts describing this behaviour at the end of the Modify ePub development thread and the implications of it, and should also be info in the Help file for that plugin.
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