Yes, symmetric rules wouldn't really work well imho.Even if you opened up the mechanism to work both ways, it feels like the New World civs in a default setup are at such a disadvantage that it doesn't really make sense. I'd rather they just have a different VC they aim for in that era. It might even open up some new gameplay options to create some exploration era civs with extra bonuses to defending that way.
If it weren't the AI we are talking about, but players in MP, I would suggest that HL civs gain economic points from bringing treasure fleets home, and DL civs gain military points from plundering treasure fleets. While HL civs gain military points from conquering in the DL, HL civs gain economic points from controlling monopolies of treasure resources for a given time.
But... I don't think the AI could deal with these.