The anodize coating is artificially induced aluminum oxide; the dye is applied before the final step seals the oxide coating. This coating should be as nearly as possible to chemically inert against anything but strong alkali or hydrochloric acid (or acid mixtures that include hydrochloric, such as aqua regia). By contrast, an acrylic coating may soften or peel in an ether solution like your collodion.
I'd recommend the 1 mm thickness; the thinner plate (IMO) is likely to bend or flex too easily (as from whatever is in the back of your plate holders to keep the plate correctly positioned, whether springs or wads of paper waste).
Unless the aluminum has been freshly cut or abraded before pouring the collodion, the naturally formed oxide layer on the back and cut edges should prevent any reaction with the silver nitrate bath, so the bath should be unaffected.
That said, I'm writing only from a chemical basis; I have no actual experience with collodion process. Black enameled or lacquered plates are the ones I see most recommended for this use -- perhaps ironically, this kind of coating was referred to, back when collodion was a current, standard process, as "Japanned".