robbehr,
I and other have offered what advice we can, in an effort to assist your learrning curve with Apples excellent iBooks Author software.
Like all software - from any supplier, it does what its designers - working to a set of instrution - engineered it to do. Apple decided on what IT as a company wanted to do with this software and in truth it does a brilliant job.
You say you have made a career change, in your situation, I think I would have been delving into all the available options and finding out what did what and if working with a combination of applications was an option.
There is a full TOC in an iBA book when viewed on the iPad. It allows the reader/viewer to move through chaptors sections and pages at will.
What you mean is, there is no TOC ( page) as is available in a paperback. You need to come to terms with an iPad that allows rapid swipe page "turnovers" select of chapters with a tap. If you want to emmulate the written book, OK..iBA does not have one or two of the printed books traditional pages.
Although I do not use either software, Apples Pages will create ePubs and the serious and smart, use Adobe InDesign.
I think at the start of your new career you need to try all your options and get to know what each of your chosen applications is capable of before taking on a paid for project.
This forum as a wealth of knowledge already in print! All you need to do is give 30 minutes a day over your coffee to search out topics and read them through.
Apple already have an update in progress based on what Apple wants next and what WE have sent in as feedback and it will come out only when its ready.
That said come September/October the new OS will allow our books to be used by computers and assuming its iTunes related means also Windows capable, which just boout triples the market.
In your favour,apart from a few models, iMacs and PC do not (yet) have touch screens so its just possibile that will be a new feature in iBA