Setting multiple VAT rates is used, when a company squares VAT in other countries, using local rates. On store page and during sales process, client from indicated country will see the same net price (because VAT does not apply to it) and slightly different gross price in comparison to the original price.
Let's use a simple example. A store sells its products with 20% VAT for £120 gross (£100 net) in the UK. After mapping this rate to 19% in B store, the same product will be sold for £119 gross (keeping its net price at £100).
Sales documents include VAT rate used in stores, the sale is made in (if mapping mechanism is inactive, the VAT rates are the same). Adequate information is also visible both in client's order and in sales reports.