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In my boat I installed the PWM Duo with battery 1 being a lead acid starter battery and battery 2 a 100ah Lifepo4. Settings only allow selecting 1 battery type however. Is the product only designed to charge 2 batteries of the same type?
And if so, what would be the right solar charger for me given 12v and 200W solar?
Mixing chemistries on the same charger or circuit is generally not possible. So you do have the wrong charger.
Probably the best solution here is to charge the starter battery with solar, then use an Orion DC:DC charger to charge the LiFePo4 from the starter. Set correctly the Orion will not drain the starter battery, but will charge the house battery when there's enough solar. It will also charge house from your alternator when the engine runs and starter is full.
