I wouldn't be concerned about permanent damage due to the oxidizing under the alcan cover. A neighbor recently bought an old aluminum skinned Shasta trailer that had sat for probably decades before he attempted to get off the oxidation. It only took lots of time and effort, but it did clean up well, and no signs of excessive damage due to corrosion. It's my understanding that BIRD POOP is a different issue. Always get that off your trailer ASAP or it will etch the aluminum. If it stays on long enough Walbernize won't solve the problem (at least not completely).
It is my understanding that the primary reasons for the raw aluminum on Camp-Inns are 1) the ability to shape it around the teardrop shaped front windows (on the 550s) and 2) the ability for it to be shaped as a skin for the galley hatch (it has to be curved along the entire length and folded on the edges - creating curves on a curve).
Supposedly Airstream has an aluminum skin that has a protective plastic coating. The upside is from a distance it always looks shiny and new. The downside is that up close after lots of use, the panels on the front of the trailer can become gravel chipped, causing oxidation to occur under the plastic coating. There is no cheap way to fix that, whereas with raw aluminum it all comes down to time, effort and Walbernize.
I, for one, wish there was at least an option to have the sides of the CIs to be a composite finish, sort of like the T@Bs that had highlight colors on the sides. It should look sharp, as long as you didn't try to make it look like the raw aluminum on the remainder of the trailer, and it shouldn't have much of an installation impact for the guys on the factory floor, since it would likely be a similar thickness to the raw aluminum. Since it is on the side, if the main use was on highway trips, there shouldn't be much problem from gravel chipping.