Hello @chipwarren Thank you for posting here. Glad to see that I am not the only one using Ghost to publish a novel!
I was able to successfully publish my novel using Ghost. While Ghost is not perfect for the novel format with a bit of massaging and some hacking I got it to work pretty well imho.
I had this same problem and my resolution was definitely a bit hacked and while it works I would not consider it a permanent solution.
I created my own theme because I did not find any good solutions with other available themes for this. My custom theme also allowed me to exclude the Novel Tags from the home page and display them where I wanted/needed them.
I too steered away from Collections as they just caused some bigger problems that left me boxed in with other things I wanted to do with my site. Where collections could have helped was a bit more organized and UX friendly layout. For example my news section is a bit odd (you have to click a link to get taken to the actual news page AFTER clicking the News button). In the end it is not a huge deal…
One issue I have with Ghost is that I cannot send an excerpt of a post sent in email newsletter. please consider voting for this here to be added to future updates of Ghost CMS.
I hope to read your novel when it is published on the web 
Cheers!