It's no different than other consumer protection laws, it only protects consumers. The law generally assumes that a business doesn't need any protection; i.e. it's on an equal status with the bank.
The fact that Reg E does not apply does not mean banks do not work with their business customers to resolve EFT problems, it simply means that they do not have to follow the regulation's time frames and moronic liability standards when they do so. I've never looked at them, but assume that the contract with the card issuer affords businesses some protection.
In this world you must be oh so smart or oh so pleasant. Well, for years I was smart. I recommend pleasant.