Those 2 lines are no longer needed. I will remove them soon.
In the early days of the WebStore project it was the only project with a dependency on GCheckout.dll, so it needed to be copied from the WebStore bin to the Web bin, but now a lot of the commerce stuff is in the core to make it re-usable across features so this dll will alreay be in Web/bin and doesn't need to be copied.
The second line is also a line of legacy code. At an earleier stage I was making separate dll for AuthorizeNETPaymentGateway.dll and planned to do the same for other payment gateways but this also changed after some re-factoring so this line isn't needed anymore either.