If he wants an additional TOC, he wants an additional TOC. Don't force your ideas on others. You can suggest, but do not force please.
I would suggest not using Calibre for the ePUB conversion. It is a great library management tool, but a mediocre conversion tool. It generates ugly code that easily can go wrong. A lot of the good ePUB makers are using Sigil to create ePUB.
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