I'm not sure what would be causing the bubbles, but any "raw" aluminum that's exposed will form an oxide layer, which is basically just what anodization is.
If you tried to "anodize" iron, for example, you'd just get a layer of rust on it (Iron oxide, FeO). Anodizing aluminum creates a layer of aluminum oxide (Al2O43) on the piece. Al2O3 is much harder than raw Al and therefore an anodized piece of Al will resist scratches & what not much better. The oxidization of Aluminum will take place anytime you have Aluminum and Oxygen in the same place, it will just take longer on your mast in the air than it would in a tank.
Small parts are easily anodized (or re-anodized) at home using a car battery charger and inexpensive battery acid for some reason only available in sufficient concentration from Sears. There are lots of articles on it on the internet, for example:
http://www.warpig.com/paintball/technical/anodize.shtml
Have fun!