Donald, if you are still reading this, are you able to confirm or deny that players who own an expansion IRL will have free access to it online?
Like every computer game ever, owning the board game version confers no special privileges online.
Well, I can't argue with that. I can say that it's a shame. Lots of things happen that have never been done before.
While I'm not arguing your point, I will say this: I don't think Dominion Online should really be considered a "computer game with a board game version." I think it's more accurate to call it an emulator. While your statement is still true (Like every emulator ever, owning the board game version confers no special privileges online), this is a much narrower statement: while there are lots of video games that get "board game versions" that really aren't the same game (e.g. look at Starcraft vs. Starcraft: The Board Game), the only board/card game emulator I could find that wasn't free was Magic Online. Admittedly, Magic Online does follow this same rule -- owning cards IRL does not grant ownership of those cards online -- so once again I can't argue with your point. But there seems to be much more room to establish a new paradigm here!
I guess this boils down to a similar point as that made by people buying books on Amazon. Lots of people who buy physical books would like to receive digital copies of the same book in the same purchase. Publishers hate that idea, because then they only get paid once instead of twice for the two different forms of the book.
I hope that, as time goes on, the march of technology will push publishers towards unification of purchases: either buy the digital thing at a discount, reflecting its negligible incremental production cost, or buy the physical thing and get the digital component as added value.
But, like I said before, even if you and your partners in the new site were willing to consider such an idea, I have no idea how you would pull it off.