Yes these contracts will be traded soley on the Bitcoin Exchange and they will have different prices namely because the price on the Bitcoin Exchange will be in Bitcoins not USD. This is no different than how commodities trade on other exchanges around the world. Ultimately the traders on the Bitcoin Exchange will be the entities that set the prices for these commodities.
The prices will be different not because of the denomination, but because traders won't be willing to risk an arbitrage on an untrusted market which makes no guarantees of delivering.
Other commodity exchanges actually trade the commodities, where the paper contracts are obligated by regulatory law to deliver in real goods at least a portion of the of the contract.
Your i2P BTC/USD market seems probable to work, because even if unable to withdraw in USD, one can already withdraw the USD elsewhere. But will anyone risk an arbitrage on an electronic market for a commodities contract with zero backing, not even one single other buyer? I might risk a tiny bit, if someone else goes first.