Thanks everyone for the responses. I realize I'm still not providing enough facts. The "standard" head tube length I was referring to is the stock head tube length for this make, model and year - 2001 Litespeed Palmares, according to a Litespeed catalog. The fork is a standard 700c fork, and has the same measurements as the fork that came standard on those models, according to the catalog. The headtube shows no signs of having been hacked apart aftermarket - whether custom or defective, it was done at the factory. The Palmares head tube has wider reinforcements at the top and bottom, and those are still in place, are the same size as each other, and appear to be the same size that I can see in photographs of other bikes of this make/model/year. The seller acknowledged, after I received the frame, that the headtube is custom. The frame has a team sticker on it, so it's possible that someone really wanted a Palmares with steeper angles (and didn't want to just buy one of the Litespeed TT models for some reason). It's just a weird thing to make custom.
The headtube extender that fuzz2050 linked to is exactly what I was thinking of. But it won't be able to get the length precise (that one is 2 cm, and I'm short 2.6 cm). I'll have to do the math to figure out whether a 2 cm adjustment will bring the bike's angles close enough to normal for me.
I think I have a pretty good case to return it, since before I bought I asked the seller about the headtube length specifically, and he answered and gave the stock catalog number, which was not true.