I don't understand what you mean by this. To my understanding, the companies' transactions/data are either on the Ethereum blockchain or not. Do you mean that they are using some other type of distributed ledger algorithm unconnected to Ethereum?
You can use the Ethereum project code to speed up and reduce the cost of development, since a lot of man-hours has gone into R&D by the Ethereum foundation (you fork the codebase). Ethereum is open source, anyone can do this. EEA members will likely run private, permissioned blockchains, likely using proof of stake or some other energy efficient consensus mechanism.
When you use a private blockchain, I like to think of it as being a bit like using a corporate intranet vs the public internet. It's disconnected, but it's possible at some point that data will flow across the public Ethereum blockchain if it's in the members' interest.
For example, imagine a private, permissioned blockchain using proof of stake for the insurance industry[1]. Since it's permissioned, only the major players get invites, and since they know each other, trust is higher than on a public blockchain. Each player has a certain number of shares/tokens, used to validate transactions. They use this to streamline their business. At some point (purely speculative on my part) they may wish to share information with some other entity who is not a part of their private blockchain. It's possible that data from the private blockchain could pass along the public Ethereum blockchain at this point, perhaps to an external auditor, regulator, other financial institution, etc.
