Hi, David...
Yes, the colour is quite confusing, isn't it...? I'd still say it's a film-related quirk, as the confirmation of Geschwaderstab status by way of the last letter 'A' in the code would, in theory, have meant the first 'A' being RLM24 blue.
As for white engine cowlings, personally I don't think so. I could be wrong of course. Technically, this would have indicated a machine operational on the southern front - southern Italy, Sardinia, Sicily and North Africa. I have seen Heinkel He111s with white engine cowlings, but I can't say I've ever seen a Ju88 similarly coloured. Wait for it... someone will probably prove me wrong in a few minutes...
Just as a little teaser, who agrees that it's a Heinkel He45 beyond the Ju88...?
Regards...