I just published my first book a couple days ago. It was published to Kindle, so not sure if this advice will be relevant to you.
Anyway, I found that editing the HTML file directly was easiest. Word and other programs seem to add in a lot of junk tags that the ebook readers discard. Plus, by looking at the HTML, you can see exactly what's going on.
For your situation, you can add the <center> tag at the start of the TOC.
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