I have never stored a rifle in a hard case inside a locked vehicle before. After removing the 209 or #11 cap of course, if it were me, I would wipe the rifle down well with a quality gun oil to remove all moisture and finger print marks. I would avoid any oil in or heavy around the muzzle or nipple area. A light wiping to clean would be all. I would also make sure the case was bone dry. But I do not think I would wrap the rifle in any plastic. I would worry that as the temperature in the case levels out, the plastic it was wrapped inmight make it sweat.
Poster .. Triple Se7en can answer this for you I believe. He has had a lot of experince with muzzleloaders, powders, and sabots. I also believe he has first hand experience in this area...
Good luck with your rifle and if you find a system that does work well, let us know. You never know when one of us will get the oppertunity to hunt somewhere and have a similar experience...