Batch auctions do defeat cross-exchange arbitrage. I went into some detail about this here: http://cdetr.io/smart-markets/ [excerpt from Section 2.1 Batch auctions and mechanical arbitrage]

> ... batch processing with uniform-price clearing eliminates mechanical arbitrage opportunities. To be clear, if only the local market utilizes batch processing with uniform-price clearing, and the external market utilizes conventional serial processing and discriminatory pricing, then there will still be arbitrage opportunities in the external market. That is, the fastest traders can still profit by propagating prices from the local market outward to the external market. But arbitrage opportunities in the other direction, from the external market into the local market, are eliminated.