Increasing the cell to an SC-60 will offer longer cell life and a linger proration warranty.
I have an SC-48 because that's what they gave me (heck it was free).

The question regarding the booster pump with your flow rate will be critical as the booster pump will draw water away from the manifold assembly and may result in a low flow condition, which will turn the Pool Pilot cell off.
How many hours per day do you anticipate running the booster pump? If it's just a few hours per day of your 12 hr/day cycle, that shouldn't affect the ability to maintain your chlorine level.
I do not recommend placing the booster pump suction downstream of the Pool Pilot manifold as the higher concentration of chlorine may (or may not) do damage to the booster pump and cleaner. I believe there are metallic components in the cleaner such as pins, shafts and screws.

Have you considered a suction side cleaner with an in line leaf trap? The leaf trap will collect the debris before the skimmer basket, and will alleviate extra debris in your pump basket and filter. That's what I have.