I have no personal experience with the Zodiac battery, but I would guess that reverse polarity protection is built into the battery cells instead of the charger in that case. Unfortunately, that's not normally the case (since it's not normally necessary).

It's true that lithium batteries have very little memory effect compared to other battery chemistries, but no battery type can completely eliminate the memory effect. Since the charge timer may kick in the battery may only be partially charged. Charging again may work, but could potentially cause the temperature sensor to terminate the charge since all batteries heat up to some degree when charging, and the amount of temperature increase is proportional to the duration of the charge. This could be solved by allowing some time between charges, but isn't the whole idea of a second battery to increase uptime? Seems like you'd be better off just keeping a spare on hand and swapping it when the first one dies. Yes, I know you would lose hot-swap ability, but what's so important that you can't shut down for a minute or so to swap batteries?

Yes, #1 could be solved by purchasing new batteries sooner, but do you really want to spend money on new batteries more often than is absolutely necessary? As for #2, the possibility is remote (and obviously worst-case) but not impossible or unheard of.