According to the information I've found, they recommend it because smart alternators only output 12.2 volts once the main battery is charged. The c-tek unit needs 12.7 V to kick in charging the second battery. The relay is connected to the solar input for the dual unit, which makes use of the MPPT regulator and allows it to draw charge at the lower voltage. If you had no solar I couldn't see an issue with hooking your alternator feed directly to the solar panel input on the d250s but if you run both you need the relay to be able to charge from either.
Cheers
Ultra
Edit:
Scratch what I said about not running one at all. According to there info you run the risk of flattening your battery because the solar input won't be looking for a low voltage to cut out on. I.e. Your relay acts as an isolator in that setup.