I don't think those bullseye fairleads have anything to do with the mainsheet. I still think the PO was using the 18" bridle to the eye straps on the top of the transom for mainsheet. Perhaps the bullseyes were for spinnaker sheets? (I know that's how the symmetrical spin sheets on my 14 footer were rigged. But that boat is generally sheeted midships, not aft at the stern quarters like a bigger boat would be. And also, it's a little boat.)
Having the attachment point for the boat end of the mainsheet aft of the boom end is how it's done on many, many boats, my O'day included. It's not going to matter, because pulling too hard on the main sheet will over-tension the leech anyway, and still not get the boom on the centerline. Again, it's not a racing boat trying to point as high as possible.
If I were putting a traveller in for mid-boom sheeting, I'd prefer to have the traveller lined up with the boom attachment point, but it's still not really necessary - in fact my friend's Beneteau First 235 has the boom attachment point offset from the traveller. Sometimes there's ideal angles, and sometimes there's "works good enough" angles...
Brian