I did some investigating on google japan and found this listing. Under the description (last box above the 39,900 yen price) it states that the stickers and plain cowl are so that you can apply them to reproduce the "DVD illustration version" of the bike as drawn by Katsuhiro Otomo (presumably this is the art/illustration DVD included in the separate white box with the decals and plain cowl as a special pre-order bonus/present). This makes sense as the sticker sheet has a lot more logos than what was on the bike in the film. And on closer look, the stickers on the proto are quite different from the sheet (ie sheet is missing the USAF style mark). Seems pointless to not include the regular stickered bike otherwise. And I want to reiterate that Bandai often releases really early proto pics (often just a CGI model) so I won't stress that most pics lack decals.
So I think we can safely assume that the regular version will have all the decals applied (and we can all give a sigh of relief and safely pre-order from somewhere other than SST). If I'm wrong, bikes for everyone on me! 冗談ばかり! (J/K)