Can you tell me why we have so limited customization?

From a historical perspective that Rise was never intended to be a fully customizable authoring tool; that task went to Storyline. It was made for very simple authoring... quick and dirty course building.

With that said, they have made a lot of improvements to Rise over the last two years, one of them being block templates. Have you tried creating individual blocks or block groups using your client's colors and saving them as block templates?

Alternatively, you can create full template courses using your clients' different styles. Whenever a client needs something, you'll have a nice starter course to work off of.

I also recommend using something like BuddyBar to manage your different palettes. It's a nice way to copy hex values in a pinch!