BTW, one of problems it creates is that when a thumbnail picture of the uploaded book is displayed somewhere, this useless first page is shown instead of the book's real cover.

I think what's happening here is that there are some JP2 files in the JP2 zip file that is used as a source for building the DJVU that should not be included.

From the scandata.xml file, we see:

<page leafNum="0">
    <handSide>LEFT</handSide>
    <pageType>Color Card</pageType>
    <addToAccessFormats>false</addToAccessFormats>
    ...
</page>
<page leafNum="1">
    <handSide>RIGHT</handSide>
    <pageType>Cover</pageType>
    <addToAccessFormats>true</addToAccessFormats>
    ...
</page>
...

Where addToAccessFormats=false denotes that that image should *not* be included in "access formats", which (AFAIK) is things like the BookReader interface, PDFs and DjVus (when available).

So, IA-Upload should read the scan data and omit any addToAccessFormats=false pages. In this case, "leaf numbers" 0 and 329.

This also causes problems with the OCR when the non-access format images are included, because the OCR text page offsets assume these pages are not included.

I just wanted to note here that not all 0000 numbered pages at IA are useless. Some are whole covers and not the scanner bed or the spine (and the spine might be useful and/or informative).

Please do not consider the elimination of 0000 images as an easy fix....

That entire scandata.xml file is currently not taken into account. You can see how the tool uses the zip files here:
https://github.com/wikisource/ia-upload/blob/1ba22eb9083f53c1118175648941a702e80b2a15/src/DjvuMaker/Jp2DjvuMaker.php#L100

If it is too hard to do an automated process, then maybe we can have an advanced functionality, Either something were we can exclude a page name, or an intermediary page where we can grab all the pages into a list, and then checkbox them for inclusion, and allow the manual deselection of pages for exclusion. It is problematic at this time that many works are pretty much excluded. I have deleted half a dozen of uploads due to this issue.

Looks like the same bug a reported in T243163.