Well, my answer there comes from FelPro, not Honda...
Auto head gasket holes look oval, too. It always appear that they are round when you remove them, years later, though. I've done this with several engines (390 V8, 200 CID I6, 351W, a couple of Toyotas...), and they were all the same, started oval or egg-shaped, ended up round. Not perfectly round, but a lot more round than when I laid them on the heads. The interesting part is the steel head gaskets on the 200 I-6, which I have been inside about 4 times, now: those steel ones go on oval and come off EXACTLY round.
FelPro says the oval holes will spread to a round shape when torqued and pressured. It's a short sentence, but that's what they say.