Re: matching headstock
The RFRs are orange-y and are listed in the 88 catalog, but were pretty much also made in 87, I don't recall if that color was in the 1987 supplement catalog with the 550s or not, but I've only really ever seen them with 1987 s/n's - come to think of it, I've never seen an RG550 with an '88 serial, except someone who mentioned a neckplate with an '88 hereon the forum recently. And, I remember when I bought my original DY (an '87 I bought in '88 ) there were a couple in the store with black headstocks - I specifically remembering making sure to tell the guy NOT one of those. I have also owned 2 Violet Pearl 550s with maple boards and black headstocks, both of which were 87s, and that color isn't even in the 87 or 88 catalogs. So, just because they weren't in the catalog that way doesn't mean they didn't make them that way. It's an assembly line of parts, there's no real magic in the process. For the DYs, who knows, maybe there was a problem with a matching color neck and they just threw on a black one, or maybe they didn't have enough, or whatever, it happens.
So for your guitar, maybe it has had the neck changed, maybe it came that way, it's just one of those things. As long as it plays and looks good, that's all that matters.