I'm guessing your pro rata battery is from Napa and you're paying full retail.
In which case, I would go for that one. I read the Napa warranty terms and they are good.
My reasoning is this:
A manufacturing defect will more likely appear sooner rather than later, so both options cover that likelihood similarly.
If something happens in the second 18 months, you'll still get a large % of your money back with the pro rata battery.
Since you're a car guy, you battery will likely last beyond 36 months so you'll get some value from the pro rata warranty.
Also, if the 36 month battery does get changed, the new battery most likely inherits the original warranty ie it does not extend it. With the pro rata battery, the replacement battery warranty starts again.