Being a dowel hole, it can't cause an oil leak. Sometimes dowel holes are blind like yours are supposed to be, and sometimes they are drilled and reamed all the way through. I don't much like blind holes because they are way too difficult to clean out when you overhaul the engine.
I suppose one could argue that all the engines should be the same, rather than some of them having the hole partly broken through like yours. Personally I would trim it into a normal round hole with a hand-held countersink tool, which seems to be what your Honda dealer wants to do. In other words, I'd prefer to see a better standard of quality control in the factory, but it is a purely cosmetic fault which I would class as trivial. I suppose even Japanese-made Hondas have those occasionally on very old models made with very old tooling.
