Phil, I think everyone means not to alodine before you prep and drill the part. Most people work with the Al the way they get it (blue plastic and all)until just before riveting it together. So, after trimming, fitting, bending, drilling, etc is finished and you are ready to rivet the parts together forever, you insert the Aulmiprep, Alodine, Prime process here, if that's what you want to do. As a side note, the only step I do after priming is dimpling. That's becaue I cannot scuff the dimples very well when using alumiprep. And the 2-part primer I use stays on very well during the dimpling process.
Say, for example, you get your kit in August but know you won't be able to touch it before next July. Should you use any surface protection to help control corrosion? You could if you wanted to, but it's unnecessary, and you'll need to do it again anyway once the parts are fitted and drilled.
Once your subassemblies are finished, like your HS for example, most people just remove the plastic and leave the part in an environment where it would dry if it got wet. So, no plastic bags or anything that prevents evaporation. Could you go an extra step and alodine the parts for storage? Sure! but it's not necessary. When you get ready to paint, your will need to do a lot of surface prep anyway, Alodining then is more convenient.
And about priming with no surface treatment other than cleaning, you should at least scuff the surface VERY well to help the primer adhere. The Alclad surface is pretty slick and doesn't hold on to primers or paint very well. If you use self-etch primer, you should still scuff with scotchbrite first.
Hope this helps