I agree that Word can be a challenging program when it comes to formatting books! I wish I could say there was a better and easier program than Word. There may be other book formatting programs or plug-ins for Word that could help, but I haven't used them. It would be just another program to buy, learn and keep updated.
Almost all of my clients (except one in the past couple of years) use Word. Also, both Createspace and KDP accept Word documents. So it's easier when all of us use the same program.
I always recommend that writers and authors develope Microsoft Word skills. If you experiment with some dedicated book formatting software, I'd love to hear about your experience.