It's an interesting situation really... "tweaking" the mold to a toy is a bigger process than one can imagine. It, as is my understanding, usually requires a new mold anyway, it's just based on an established sculpt. Not sure on that, as I don't know specifically how capable Hasbro's manufacturing facilities would be to actually just alter an existing mold, but I know other companies are not capable of doing that... So I'd think Hasbro would be limited in that way, but who knows.
Scott's right though, it boils down to it being more work than just ordering the manufacturer to alter the paint application order...
One could say, "well yeah, but it'd cost more", but the reality is that the profit margin on sets like this is so spiffy for Hasbro, that it is a bit frustrating that one new "tweak" isn't done. I doubt a new head mold for astromechs would really make the sets less of a success for everyone involved, ya know?
Another factor though, and maybe a good one to NOT get R5-D4 in these, is that maybe Hasbro felt R5 should be a basic figure... sorta released en masse. I know customizers will have a field day with the figure when it's eventually released... Astromechs seem to be kind of popular, and almost like army builder figures. Just a random thought.
I agree that the dome wouldn't cost them enough to be cost prohibitive... Those sets are profit with really negligible costs. That's what sucked so bad about the EE Clone set's price to me. Short of them being REALLY limited production items, which I don't bite.