The command interface is different and not inter-compatible for both devices. The sampling and configuration commands are also not inter-compatible. Because of this, they require different software (i.e. SeaFETCom for V1, UCI for V2).
The SeaFET/SeapHOx V1 has native USB compatibility, while the V2 is an RS-232 only device. The V2 requires a USB-to-RS-232 adaptor to connect to a USB port.
The magnetic switch serves different functions on a V1 versus a V2. The V1 uses it to activate & deactivate the internal batteries, but the V2 uses it to provide sample status.