For us it is two-fold:
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To fit the official corporate house style such as color, font, typography, logo and layouts for websites and documents. I think this is common for many businesses, even if not formalized as we do, most of them would use some kind of branding to make them stand-out from others. For example letterheads, websites, invoices, etc are immediately recognizable amongs a heap of competitors. Internal compliance with the housestyle is a must and therefore one needs the ability to customize themes.
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To present information using logic and where needed calculations that are specific to a business and fits their corporate style and can not be added or appear in the right location when using custom fields.
I noticed that we can still create and customize themes so the core functionality is there. However, the example themes that existed were useful to quicker achieve the desired results.