>>>What if this wants to be applied to only the Development environment? This might means every time there is a change in the interface and we need to transport it to the QA environment, we need to remove the second receiver before transporting it, and set it back again after the transport
Your assumption is correct. You must remove the second business system as it's only for development environment else it would fail.
>>>What about for outbound from ECC interfaces? If we need 2 BS for each ECC system, it will be tedious too..
Same like other ECC system. You'll have to maintain the IS_URL(sxmb_adm) and configure RFC destinations&partner profiles which will point to PI system.
At least for outbound you don't need to do much as you don't need to transport them.