It is cheaper and better but stock holders usually have investments in tens and even hundreds of different entities - each of them having its own system is not most convenient and most likely not the cheapest solution for the investor. When exchanges do become available offering the same benefits as those in-house solutions as the Overstock/IBM ones, it will be hard justifying using only their in house exchange.
It would be annoying (and can add up in fees) to use cross-chain trading to move currency from one company's stock exchange to another all the time for a trader.
In addition, with a blockchain cryptostock that the company has full control over, it ends up being no different than a centralized exchange solution: you need to trust your currency held in the exchange (whether to buy the stock or the money received from selling it) with the company running that exchange. The whole point of the decentralized exchange is that we no longer need to trust companies with our money in order to trade. Also, it is not clear that the company would want to deal with the added liability of safely holding the trader's funds.
I think there would be multiple stock exchanges DACs (for scalability reasons) but not too many because of the inconvenience of doing atomic cross-chain trading of BitCurrencies from one blockchain to another.