Bill Traynor pointed me at this and the author wrote this in the comments about what he’s using:
I wrote the book in Markdown and styled it with CSS thanks to PrinceXML (via DocRaptor). This framework stitches everything together and translates it to different formats: https://github.com/jstorimer/kitabu
I’m using Shopify for the e-commerce software and Fetch app for digital delivery. I’ll stick with Shopify but am going to try something new for delivery soon. Those numbers don’t include the Kindle sales. My current total royalty from Kindle sales is ~$250 USD. I’m not sure of the sales volume but I certainly get much less per-sale there.
Someone else in the comments mentioned http://pulleyapp.com for book delivery.