The closer in the moon orbits, the faster its orbit. So, even though it may be totally covered by the shadow of the Polyphemus when it is behind it, it doesn't stay there for too long. It's never in the shadow long enough to really cool it down to any extent...and with 18% CO2, the heat distribution and retention throughout the atmosphere would be very effective. The moon wouldn't lose much heat at all. However, if it was at a distance from Polyphemus where the moon was eclipsed for a considerable period of time, because of its slow orbital motion, it may cool somewhat. Polyphemus covers about 20% of the moon's sky, which would put it at about 3.41 million kilometres. At that distance, it would orbit the planet in about 6 days or so. At it's orbital velocity, it wouldn't stay any longer than 30-36 hours behind the planet before it emerged into bright sunlight. That length of time wouldn't be enough for the moon to cool considerably with such a CO2 rich atmosphere. Not only that, Pandora does rotate but the rotation is not locked to its orbital motion (spin-orbit coupling), so the moon never has any one side facing the planet all of the time.
The moon would never get as close as the top of the planet's atmosphere... that would be well within the Roche Distance of the planet-moon system and Pandora could be pulled to shreds (if it orbited permanently that close). Actually, given Pandora's size, it would most likely plunge into the giant intact and the resulting collision (as it would penetrate right to the core of Polyphemus...given its size) would give the giant planet a lot of grief. It would seriously disrupt the giant.
For Pandora to cool significantly in the shadow of Polyphemus, it would have to linger in that shadow for a week or more. I could work out how far away it would have to be, exactly, but I don't feel like doing it right nowHowever, it would have to be about 20-30 million kilometres from the giant, at least, for it to linger for a week or so in its shadow. That far away from Polyphemus would probably put Pandora in the gravitational influence of Alpha's outer giant planet because of orbital resonances and such. That would make Pandora's orbit unstable and the moon would've either crashed into the giant or got flung out of the system altogether.
